Stargate Atlantis: The Complete Series

The Stargate SG-1 team discovers what they believe to be the remnants of the lost city of the Ancients - the originators of the Stargates and Stargate Command launches an investigation to find the mythical city of Atlantis. Situated in the distant Pegasus Galaxy - farther than any Stargate team has ever traveled. With only enough power to make a one-way trip a new team headed by civilian Dr. Elizabeth Weir (Torri Higginson) is formed and travels through the gate to this unknown galaxy. There they discover the marvels of the lost city of Atlantis… and encounter a sinister new enemy.

Dr. Rodney McKay (David Hewlett) undergoes experimental gene therapy altering his DNA to match the Ancient genetic coding. The experiment opens up countless scientific possibilities as well as an unexpected problem. Meanwhile during a game of hide and seek one of the Athosian children inadvertently opens a containment unit that lets loose a seemingly harmless black ethereal cloud. But when Atlantis goes through a series of technical malfunctions they realize that the shadowy creature is actually feeding off of the power supply!

Fleeing from a surprise encounter with the Wraith Major Sheppard (Joe Flanigan) falls victim to an alien symbiote which is feeding off his life force and slowly paralyzing him. While speeding back to Atlantis for medical aid the team gets trapped halfway through the Stargate when the puddle jumper damaged in the altercation with the Wraith suffers a mechanical failure. With only thirty-eight minutes before the Stargate shuts down Lieutenant Ford (Rainbow Sun Francks) and Dr. McKay (David Hewlett) struggle to manually fix the problem. As the clock ticks away the Atlantis team must come together or perish in the harsh vacuum of space.

Relationships are torn part when the Athosians are accused of harbouring a spy.

During an exploratory mission the puddle jumper's electrical systems are knocked out by a massive electromagnetic field and the team is forced to make an emergency landing. They soon encounter a primitive tribe of children who have been untouched by the Wraith for centuries due to the protective force of the electromagnetic field. But the children believe it is their ritual of mandatory suicide at the age of 25 that keeps the enemy at bay despite the contrary insistence of the Atlantis team. Fearing the full growns in their midst will attract the Wraith the villagers become anxious for their unexpected guests to leave as soon as possible. But to be able to leave Dr. McKay (David Hewlett) must first disable the electromagnetic field. In doing so he unwittingly trips a Wraith silent alarm leaving the tribe open to attack.

The Atlantis team encounters the Hoffans a human civilization in the process of rebuilding their society since the last attack of the Wraith. The resilient Hoffans have developed the beginnings of a drug that could potentially make them immune to their enemies. Fearing that the next Wraith culling will come before they are able to complete their tests the leaders demand that their people be inoculated before the drug can be proven safe. Dr. Beckett (Paul McGillion) argues that there is no way to know what the true effects of the drug will be. Can Beckett make the Hoffans see reason or has their haste made them blind to the epidemic they may be unleashing upon themselves?

With the city's food supply dwindling the Stargate Atlantis team must search for an alternate food source. The team begins negotiation with a simple group of farmers known as the Genii. Untrusting of outsiders the Genii are hesitant to any sort of trading--until Major Sheppard (Joe Flanigan) demonstrates the team's advanced weaponry. A deal is struck to exchange food for explosives. But upon returning to the Genii village to make the exchange they stumble upon technology that leads them to believe the Genii are not at all what they seem.

During an exploration of a planet with no apparent inhabitants Dr. McKay (David Hewlett) discovers that the planet's fog-like atmosphere is actually pure energy--enough to open a wormhole back to earth. Wanting to be sure they could return to Atlantis to continue their mission Dr. Weir (Torri Higginson) relays a message back to Stargate Command. They are told that the battleship Prometheus has been outfitted with a hyperdrive and they would be able to return to Atlantis within a month! Back on Earth the team is overjoyed to be with the things and people they love. However when the Prometheus' hyperdrive is accidentally destroyed their hopes of ever returning to Atlantis are suddenly dashed.

The team learns that a storm of catastrophic proportions is headed straight for the city of Atlantis. Without enough energy to power the shields Dr. Weir (Torri Higginson) orders that Atlantis be evacuated until the storm passes. But Dr. McKay (David Hewlett) conceives of a last minute plan to save the city--harness the power of the electrical storm to fuel the shields. Meanwhile unbeknownst to the Atlantis team the Genii have learned of AtlantisΓÇÖ evacuation and devise a dangerous plan to take over the cityΓÇÖs weapons for themselves. With Weir and McKay taken hostage and Lt. Ford (Rainbow Sun Francks) and Teyla (Rachel Luttrell) aiding the evacuees it is up to Major Sheppard (Joe Flanigan) to shut down the remaining grounding stations and save Atlantis from invasion before the storm hits.

As the storm approaches Commander Kolya of the Genii who has seized Atlantis is about to shoot Dr. Weir. Suddenly Dr. Rodney McKay steps in front of the gun and convinces Kolya that he and Weir are the only ones who can fix Grounding Station 3 the last of the four grounding stations that must be disabled so that lightning from the storm can be channeled into the shield generator to power up the shield and protect Atlantis from being obliterated. Kolya spares their lives but contacts Maj. John Sheppard over the radio and tells him that Weir is dead. Sheppard vows to kill Kolya. Meanwhile on the mainland Lt. Aiden Ford Teyla and Dr. Carson Beckett are waiting out the storm in a Puddle Jumper. Suddenly the wind stops and the sky clears. They are in the eye of the storm. Ford commands a reluctant and frightened Beckett to fly the Puddle Jumper straight up the eye over the storm to Atlantis to help Sheppard. On Atlantis a female Genii named Sora reports to Kolya that Sheppard has killed three more of their men. Weir and McKay who are working to bypass the broken switch on the grounding station overhear the conversation and try to stall the repair to give Sheppard more time. Kolya commands Sora to radio Chief Cowen leader of the Genii to send a full company of 60 men through the stargate dashing Weir and McKay's hopes of rescue. Atlantis is powered by five small Naquadah generators each responsible for a separate area of the city. Two of the generator rooms are conveniently located near transporter stations. Sheppard disables the generators powering stargate operations and Grounding Station 3 making it impossible for McKay and Weir to finish their task. Sheppard then storms the control room and raises the 'gate shield. Only five of Kolya's 60 men get through. The rest are destroyed by the shield. The storm is less than an hour away. Kolya radios Sheppard with a proposition. If Sheppard doesn't restore power to Grounding Station 3 in the next 10 minutes Weir really will be killed followed by McKay 10 minutes later. Sheppard relieved to hear Weir's voice has no choice. Joined by Ford Teyla and Beckett he restores power to Grounding Station 3. McKay is disables the station. In the control room Kolya orders McKay to power up the shield. McKay and Weir bluff Kolya into believing that McKay's plan has failed and that Atlantis is lost. He decides to withdraw but also to take Weir and McKay with him. Sheppard and Ford storm the control room and take out Kolya's remaining men. Kolya uses Weir as a human shield and backs toward the activated stargate. Sheppard takes the shot and hits Kolya who releases Weir as he falls backward through the 'gate. With the storm due to hit in 2.5 minutes Teyla and Beckett are unaccounted for. That's because Sora has knocked Beckett unconscious and is fighting Teyla whom she believes to be responsible for her father's death. Teyla wins but lets Sora live. Sora follows Teyla who drags Beckett to the control room. Weir gives McKay the order. Lightning strikes Atlantis and floods the corridors. The shield activates just before a huge wave hits the city. Atlantis is saved and Weir orders Sora held as a prisoner.

Leading an exploration of an ancient weapons satellite in deep space Major Sheppard (Joe Flanigan) and Dr. McKay (David Hewlett) intercept a Wraith distress signal. Deciding to investigate the team lands on a nearby planet and finds the source of the call - a downed Wraith cargo ship. When the unseen Wraith awakens from hibernation Sheppard and McKay become the focus of its ravenous appetite.

While assessing the structural damage to the city caused by a massive storm two of Dr. McKay's (David Hewlett) team of scientists experience horrifying visions. Minutes later they drop dead. Retracing the steps of the dead scientists McKay and his team find an Ancient lab its contents in disarray. Afraid of a viral outbreak Dr. Weir (Torri Higginson) places the city under a self-regulated quarantine. Even with the city under lockdown under the threat of a possible viral outbreak more and more people begin suffering from the same terrifying visions. If McKay cannot find a cure the entire city will be doomed.

Engaged in combat the Atlantis team's puddle jumper is hit with an energy wave that leaves them unharmed but destroys their Wraith attackers. Hoping to find the source of the wave the team lands on the planet below. There they find a civilization enjoying the utmost health and happiness untouched by the Wraith. Their leader Chaya refuses to allow anyone other than her own people the sanctuary and safety from the Wraith that would be found by settling on their planet. Unwilling to give up so easily Major Sheppard (Joe Flanigan) asks Chaya to reconsider. After thinking it over Chaya surprises everyone by requesting to accompany them back to Atlantis to discuss the matter further leading the team to suspect they may be caught in a trap.

While exploring the city the Atlantis team discovers a stasis chamber holding a woman who appears to be over 10 000 years old. Excited at the possibility that she is one of the Ancients the alien race that built Atlantis the team decides to bring her out of stasis despite the risk to her health. Everyone is shocked when once re-animated the elderly woman identifies herself as none other than Dr. Weir (Torri Higginson).

The Atlantis team travels to Dagan a planet with a hidden ZPM and a mysterious trail that will lead to its hidden secret chamber location. But the Genii have learned of the Atlantis team's activities on Dagan. Realizing the ZPM must hold awesome power the Genii plant a sleeper agent amongst the Daganians aiding the Atlantis team on their search. Now as the Atlantis team closes in on the location of the ZPM the Genii close in on them.

Having learned that the entire Wraith armada is headed towards the city the Atlantis team prepares to send a data message to Earth with information about the Wraith threat and what could be their last messages home to loved ones. As the rest of the team records their touching and often humourous messages back home Major Sheppard (Joe Flanigan) and Teyla (Rachel Luttrell) embark on a reconnaissance mission where they witness the vastness of the Wraith army and look on helplessly as the Wraith cull the planet's helpless inhabitants.

Terrifying nightmares about the Wraith cause Teyla (Rachel Luttrell) to lash out at her colleagues and prompt her to seek professional advice. With psychological guidance she discovers that she can sense the Wraith. In their search to learn more Teyla and the Atlantis team discover important information that may hold the key to understanding their enemy including the disturbing possibility that Teyla's connection to the Wraith could be the result of genetic experimentation.

With the Wraith armada closing in on Atlantis Dr. McKay (David Hewlett) and a small team attempt to repair an ancient weapons satellite in the hopes of leveling the odds in the coming battle. Meanwhile tension builds between Teyla and some of the other members of the Atlantis team over her connection to the Wraith. Major Sheppard (Joe Flanigan) steps in to defend her but even he begins to harbour doubts when a team member is left unconscious after an attack by an unknown assailant.

With the Wraith armada bearing down on the city the Atlantis team prepares to evacuate. Setting the city's self-destruct sequence they hope to make it impossible for the Wraith to gain access to Earth. Things begin to look up when reinforcements from Earth are brought in and it is announced that the battleship Daedalus will arrive in four days. However when the warheads are easily destroyed by the Wraith and the first wave of Wraith attackers strafe the city with weapons fire it becomes increasingly clear that the added reinforcements are not going to be enough. With time running out the Atlantis team must turn to the least likely source of aid--the duplicitous Genii! But with the Wraith overrunning the city even the Genii's help may not be enough.

Rescued from a near-fatal encounter with the Wraith Lt. Aiden Ford (Rainbow Sun Francks) receives medical care at the Atlantis base. However his abnormally quick recovery leads Dr. Beckett (Paul McGillion) to worry that the Wraith who attacked Ford may have injected him with a harmful enzyme causing long-term and unpredictable damage. Meanwhile as the Wraith's siege of Atlantis rages on Sheppard (Joe Flanigan) finds himself surrounded by the enemy. He is rescued by the timely arrival of Colonel Steven Caldwell (Mitch Pileggi) commander of the Daedalus. Launched from Earth and sent in to assist the Atlantis team during battle the Daedalus helps to defeat the Wraith's first wave assault on the city. Their relief is short-lived however. The team soon learns that the Wraith are planning the next wave of their onslaught -- an entire fleet is about to descend on the city. With a little over a day before the assault Dr. Weir (Torri Higginson) realizes that the Daedalus will not be enough to fight the Wraith's forces. McKay (David Hewlett) devises a drastic plan - but there may not be enough time to perfect the complicated technology his plan requires before the Wraith arrive.

When a scientist is killed in the Daedalus' computer room McKay (David Hewlett) first believes the poor circuitry is at fault. However when another scientist is killed while investigating the death McKay begins to suspect that someone--or something--is deliberately planning these breakdowns. Soon after McKay is alerted to a virus on one of the ship's computers. When he runs its code through a translator he is shocked to discover that it is written in Wraith. Even worse he learns that the virus has the ability to re-write itself making it seemingly impossible to conquer. Realizing that the program's capability to mutate has virtually given it a mind of its own McKay worries that the Wraith may use the virus to take control of the ship--with potentially deadly results. As feared the virus' artificial intelligence soon takes control of the Daedalus' auxiliary ships and the crew becomes increasingly powerless to defend themselves. Fearing that the Wraith will use the Daedalus' advanced features to attack Atlantis McKay and Sheppard (Joe Flanigan) race against the clock to counteract the virus before the Wraith turn the Daedalus' advanced technology against the city.

When a routine off-world science mission comes across a mutilated Wraith carcass the team suspects Ford may be involved. Intrigued they split into teams to investigate. Teyla (Rachel Luttrell) and Sheppard (Joe Flanigan) encounter Ronon Dex (Jason Momoa) a fierce warrior who survived a battle with a Wraith seven years earlier and has been on the run ever since. When Dex reveals to Teyla and Sheppard that Ford (Rainbow Sun Francks) has taken up residence on the planet they enlist his help to locate their friend. The duo hope to rehabilitate Ford to his former state. McKay (David Hewlett) eventually stumbles upon the increasingly incoherent and maniacal Ford and tries to reason with his former colleague and friend. However McKay begins to see how far gone Ford has become -- addicted to the enzyme injected in him by the Wraith who attacked him Ford has been brutally killing Wraith to get a fix of the solvent. Reluctantly McKay and the rest of the crew must face the realization that they may never be able to save Ford from what he has become.

During an investigation of a planet leveled by a Wraith attack McKay (David Hewlett) and new security team member Lt. Laura Cadman (Jamie Ray Newman) are transported aboard a Wraith Dart which subsequently crashes. Unfamiliar with the Wraith technology Atlantis scientist Dr. Zalenka (David Nykl) is only able to transport McKay out of the rubble. Cadman's body is nowhere to be found. Zalenka believes that she is still trapped inside the Dart until McKay claims to hear her voice--coming from inside his own head! It seems that Zalenka's experiment rather than saving the two separately caused them to unite--and Cadman must remain inside of McKay's head until Zalenka can figure out a way to separate the pair. Meanwhile as Ronon Dex (Jason Momoa) settles in at Atlantis he shows off his impeccable fighting skills during arsenal training. Impressed Sheppard (Joe Flanigan) implores Weir (Torri Higginson) to put aside her reservations about the newcomer and consider allowing Ronan to join the Stargate Atlantis team.

When the Atlantis team sets out to a distant planet they land on a small island off the main coast and are attacked by a group of savages. Barely escaping the island with their lives the team is rescued by one of the planet's security vessels and brought to the considerably more civilized mainland. Once safely on shore the team learns that the island had been set aside for the banishment of prisoners and is susceptible to Wraith attacks. The rest of the planet however is immune to such Wraith assaults. Intrigued by this as well as by the planet's unconventional energy source the team tells Weir (Torri Higginson) of their discovery. However when Weir arrives on the planet to investigate further she begins to suspect that the mainland's idyllic environment may be the result of a sinister pact between the planet's leader and the Wraith.

While doing standard recon on a planet thought to have been destroyed by the Wraith long ago the team finds an Ancient structure standing intact amidst the ruins. After some investigating they discover that the monolith served as a military research facility where the Ancients worked to develop an advanced method of harnessing energy. When the Wraith attacked before the project could be completed the underdeveloped technology malfunctioned and destroyed the civilization. McKay (David Hewlett) theorizes that if the powerful technology is fully developed it could serve as a potent source of energy for Atlantis. Hope turns to fear however when McKay's first attempt at reviving the energy source results in the death of one of the Atlantis scientists. Despite the team's apprehension a determined McKay insists on moving forward with finishing the project. But can McKay unravel the intricacies of the Ancients' technology without putting himself and Sheppard in mortal danger?

During a visit to a distant planet the team discovers a village whose inhabitants live in fear of a Wraith residing in their midst. When the team sets out to confront the creature they encounter Zaddik (John Innes) a scientist who has been living with Ellia (Jewel Staite) a Wraith child for the past several years. Zaddik has developed a serum that works to satiate the young Wraith's appetitie and prevent her from feeding on him. Dr. Beckett (Paul McGillion) is intrigued by the serum having been eager to test an experimental retrovirus of his own that could give the Wraith humanlike qualities and rid them of their predatory instinct. Beckett meets with Zaddik and his supposedly tame Wraith companion hoping he can begin a controlled experiment on Ellia. However when Ellia downs his retrovirus the underdeveloped formula has the opposite of the desired effect.

Within hours following his encounter with the mutated Wraith child Ellia (Jewel Staite) Sheppard (Joe Flanigan) is shocked to find that his wounds have disappeared without a trace. Soon after he begins exhibiting other symptoms similar to the ones that plagued Ford following his own Wraith attack. Dr. Beckett (Paul McGillion) realizes that a small amount of the retrovirus that Ellia ingested is now in Sheppard's bloodstream -- and he is quickly mutating into the very creature that attacked him. As Sheppard becomes less lucid by the hour the team races against the clock to save his life and reverst he effects of the retrovirus.

When Atlantis's deep-space sensors detect the Aurora an ancient Atlantian warship at the edge of the galaxy Sheppard's team wastes no time hitching a ride to it aboard the Daedalus. Upon their arrival they encounter a Wraith scout ship. They destroy the scout before it can cause trouble--or so they hope. Sheppard leads his team onto the derelict warship where they discover hundreds of crewmembers frozen in stasis pods. Although technically alive the Atlantians are thousands of years old and their aged bodies can't survive the defrosting process. Still there might be a way to talk to them: McKay discovers that all the pods are linked by an active neural interface allowing the crew to coexist with each other in a virtual environment.

While exploring a new planet Sheppard McKay Teyla and Ronon are ambushed by a group of men armed with Wraith stunners. They awaken to find themselves prisoners in a cave where they discover the mastermind behind the attack: Lt. Aiden Ford. Ford was last seen being captured by a Wraith dart after overdosing on a powerful Wraith enzyme. Now Ford invites his former teammates to enjoy a meal while he tells them how his enzyme-enhanced abilities allowed him to escape. Since that time he has recruited a group of followers all of whom are willingly addicted to the drug. To the team's horror Ford then announces that their meals are laced with the enzyme. Determined to prove that the enzyme is both safe and useful Ford intends Sheppard's team to be his living evidence and he expects Sheppard who remains free of the drug to be his witness.

Captured by the Wraith Sheppard (Joe Flanigan) Teyla (Rachel Luttrell) Ronon (Jason Momoa) and Ford (Rainbow Sun Francks) are being held hostage aboard a hive ship. As the team desperately searches for some means of escape they are shocked to discover a coalition of Wraith followers on board the ship. McKay who is still stranded on Ford's planet soon realizes that the team has been captured. In order to escape the planet he comes up with an unconventional plan: he injects himself with a massive amount of the dangerous Wraith enzyme. The drug provides him with brute strength and after knocking the guards that surround him unconscious he is able to dial the gate and leave the planet. When he arrives on Atlantis completely incoherent Dr. Weir (Torri Higginson) and Dr. Beckett (Paul McGillion) put him under immediate medical supervision. Once recovered McKay is able to calculate the location of the ship upon which the team is stranded. As tensions rise on the hive ship between the Wraith and the Atlantis team he and Caldwell (Mitch Pileggi) must devise a plan to bring the rest of their team to safety.

After detecting an energy spike over a forested area on a distant planet the Atlantis team decides to investigate. Their travels lead them to a portal built into a rock wall with Ancient carvings and a portal built into it. Intrigued Sheppard decides to test the portal to see where it leads and before he can stop himself is pulled through to the other side with no way to get back or communicate with the team. When no rescue team comes through the portal Sheppard explores his surroundings and he encounters Avrid (David McNally) a man on the run from a dangerous creature. After a violent showdown Sheppard succeeds in warding off the creature. Avrid then brings the injured Sheppard back to his home to recover. There Sheppard discovers that all the inhabitants of the planet are direct descendants of the Ancients and he is the only one ever to have survived such an attack. Meanwhile the rest of the Atlantis team is trying to figure out what happened to him. After translating the writing on the rock wiht the help of some Ancient textbooks Weir (Torri Higginson) discovers that Sheppard has been transported into a time dilation field designed by the last of the Ancients as a sanctuary from the Wraith -- a place where people could live in peace and saftey and ascend to a higher plane of existence. However there are also a warning inscribed on the stone: once the threshold across the portal is crossed there is no return.

General Landry (Beau Bridges) informs the team that the Goa'uld have planted a bomb on Atlantis and will be triggered by any attempt to dial the gate. After some investigation McKay (David Hewlett) determines that the failsafe mechanism on Atlantis' energy source hase been disabled -- so any action that might cause it to overload (such as dialing the gate) would result in an explosion. Furthermore the mechanism is now locked with an unbreakable code and they must find the individual who tampered with it in order to enable it once again. To make matters worse two Wraith cruisers are headed straight for Atlantis. They must activate the cloak in order to keep the city invisible to the Wraith - but such an operation would surely cause the energy source to detonate. With time running out an alarmed Weir (Torri Higginson) launches a full-scale investigation to find the saoteur. She is shocked when she discovers that the perpetrator is a member of her own team.

On a puddle jumpter test flight McKay (David Hewlett) and a pilot suddenly lose control of the ship and crash into the ocean. Though he is able to communicate with Weir (Torri Higginson) he soon loses contact with Atlantis as he sinks lower and lower. Trapped in the back of the ship with almost no power and a badd concussion McKay begins to hallucinate. Fortunately for him his hallucinations come in the form of his intellectual rival Samantha Carter (Amanda Tapping) who is ready to assist him in finding a way out. However before they have time to formulate a plan t he jumper descends to the ocean floor and the impact causes a small break in the ship's hull allowing water to sink in. Meanwhile back on Atlantis Weir and Sheppard have located McKay and devise a plan to rescue him -- but will they reach him before time runs out?

During a trade mission on a distant planet the team is introduced to a village with a central tower -- one almost identical to the central spire of Atlantis -- inhabited by the village's revered leader who is able to protect the people that live there from the Wraith. Intrigued the team inquires about meeting this Lord Protector but the overly suspicious guards surrounding the tower capture Sheppard (Joe Flanigan) and confiscate the others' weapons. Inside the tower Sheppard is introduced to the dying Lord. When the Lord and his advisors discover that Sheppard also possesses the Ancient gene needed to protect the village they decide that he should marry into the family and become the Lord's successor. While McKay (David Hewlett) investigates the source of the Protector's power the Atlantis team tries to free the people from this unjust ruling family but is unwittingly caught up in a devious power play.

On the way to investigate a potential source of energy the team encounters two pods in orbit around a moon. They decide to take one back to Atlantis for observation. Upon opening the pod they find a woman in stasis. As they speculate about her age an energy beam emanates from the pod and hits Weir (Torri Higginson) allowing her to harbor the consciousness of the woman inside the pod. Through Weir the team learns that the woman Phoebus was from a race of explorers whose vessel was attacked by the Wraith. She claims that the body of her husband Thalan occupies the second of the two pods found by McKay and her wish is for the team to bring him back to Atlantis so that Sheppard (Joe Flanigan) may harbor the man's consciousness and allow him to communicate one last time with his wife. Unfortunately once the plan is put into action the team learns that it was all a ruse: Phoebus and Thalan were enemies and her real intent was to have the team revive Thalan so she could finally finish him off. Now as Phoebus and Thalan wreak havoc throughout Atlantis in the forms of Weir and Sheppard the rest of the team must find some way to stop them before they destroy each other - and Atlantis itself!

When a village on a distant planet is ravaged by fire the team is called in to investigate the damage. In the attack Major Lorne a member of an off-world team working there has seemingly disappeared. Upon further investigation Teyla (Rachel Luttrell) and Ronon (Jason Momoa) find a wanted list circulating about the village--and on it is Major Lorne's name--along with those of Sheppard (Joe Flanigan) and McKay (David Hewlett). Weir (Torri Higginson) quickly deduces that whoever composed it was seeking people with the Ancient certain gene that provides the ability to operate Ancient technology including Ancient ships. Compounding matters the team is contacted by Ladon Radim a former Genii. Now claiming to have severed ties with Atlantis' old foe Ladon has an offer: a valuable zero point module in exchange for their help in planning a coup against the Genii. Ladon claims the Genii have been harboring nuclear weapons and are becoming an even greater threat. Skeptical of what they've been told the team decides to alert Cowen the Genii leader of Ladon's plans. Cowen confirms that Ladon is no longer linked with the Genii and thanks the men for the warning. Satisfied that the Genii pose no immediate threat Sheppard and McKay plan a raid to simply appropriate the ZPM from Ladon. However when they arrive their team is taken hostage by Ladon and Cowen who are after all still Genii accomplices. Their plan is to negotiate for Atlantis' Jumper ships which they intend to use to attack the Wraith. Now Weir must negotiate with the Genii--before it's too late.

Sheppard's team visits the planet Taranis at the invitation of two leading citizens Dr. Norina Pero and Chancellor Lycus who want McKay to repair a failing shield generator at an Ancient base they've discovered. Lycus also shows the team a massive Ancient warship much like the Aurora hidden in a vast warren of tunnels beneath the base. Although the warship is damaged and currently inoperable Dr. Weir eagerly opens trade negotiations with Lycus as soon as she learns of its existence. As mysterious earthquakes rattle everyone's nerves McKay overcomes his attraction to Dr. Pero long enough to discover that her people have seriously overtaxed the shield's capabilities. Worse the shield's energy source is the magma chamber of a supervolcano beneath the base--a volcano that has been destabilized by the excessive energy demands. A catastrophic eruption is now imminent: Half the continent is about to be ripped apart rendering the entire planet uninhabitable. Everyone must evacuate. As the earthquakes grow stronger local villagers begin arriving at the base through the relative safety of the Ancient tunnels. Weir and Lycus lead some of them through the stargate to Atlantis but seconds later the ground around the 'gate erupts. The stargate sinks forever into a pool of molten rock. From Atlantis Weir immediately dispatches the Daedalus to Taranis but it will require multiple trips to evacuate everyone. Sheppard and McKay knowing that they don't have that much time start repairing the Ancient warship while Teyla Ronon and Dr. Beckett hurry to a nearby settlement to organize the first group of evacuees. Soon after the Daedalus departs from Taranis new vents erupt ash starts falling and the outside air turns toxic forcing Beckett Teyla and Ronon to send the remaining villagers through the tunnels to the warship. Then McKay discovers that a lava flow has sealed the main hangar doors shut. Now even if he can repair the ship they'll still have to find a way past this molten barrier. Teyla and Ronon remain in the settlement until they've rounded up the very last of the villagers only to be trapped when the tunnel that leads to the base collapses. As the duo fights to stay conscious in the deadly air Sheppard notices that they're missing and descends into the maze of tunnels to find them. Soon he's cut off too--and even if he somehow makes it back there's still no guarantee that McKay can even get the warship off the ground.

Sheppard's team visits the planet Taranis at the invitation of two leading citizens Dr. Norina Pero and Chancellor Lycus who want McKay to repair a failing shield generator at an Ancient base they've discovered. Lycus also shows the team a massive Ancient warship much like the Aurora hidden in a vast warren of tunnels beneath the base. Although the warship is damaged and currently inoperable Dr. Weir eagerly opens trade negotiations with Lycus as soon as she learns of its existence. As mysterious earthquakes rattle everyone's nerves McKay overcomes his attraction to Dr. Pero long enough to discover that her people have seriously overtaxed the shield's capabilities. Worse the shield's energy source is the magma chamber of a supervolcano beneath the base--a volcano that has been destabilized by the excessive energy demands. A catastrophic eruption is now imminent: Half the continent is about to be ripped apart rendering the entire planet uninhabitable. Everyone must evacuate. As the earthquakes grow stronger local villagers begin arriving at the base through the relative safety of the Ancient tunnels. Weir and Lycus lead some of them through the stargate to Atlantis but seconds later the ground around the 'gate erupts. The stargate sinks forever into a pool of molten rock. From Atlantis Weir immediately dispatches the Daedalus to Taranis but it will require multiple trips to evacuate everyone. Sheppard and McKay knowing that they don't have that much time start repairing the Ancient warship while Teyla Ronon and Dr. Beckett hurry to a nearby settlement to organize the first group of evacuees. Soon after the Daedalus departs from Taranis new vents erupt ash starts falling and the outside air turns toxic forcing Beckett Teyla and Ronon to send the remaining villagers through the tunnels to the warship. Then McKay discovers that a lava flow has sealed the main hangar doors shut. Now even if he can repair the ship they'll still have to find a way past this molten barrier. Teyla and Ronon remain in the settlement until they've rounded up the very last of the villagers only to be trapped when the tunnel that leads to the base collapses. As the duo fights to stay conscious in the deadly air Sheppard notices that they're missing and descends into the maze of tunnels to find them. Soon he's cut off too--and even if he somehow makes it back there's still no guarantee that McKay can even get the warship off the ground.

A Wraith hive ship arrives in orbit above Atlantis. In the cloaked city below everyone is stunned when Michael radios down with an unnerving request: He wants to negotiate an alliance. Frustrated in their quest to locate Earth the Wraith are now running short of their food--humans--and have begun fighting among themselves. For this reason Michael seeks a weaponized version of Dr. Beckett's anti-Wraith retrovirus which briefly gave him a human body. He wants to deploy it against rival hives turning them human and feasting on the results. His hive will gain food and power and the Atlantis team can deal a fatal blow to thousands of their enemies. Weir and her senior staff decide that such a payoff is worth the immense risk of trusting the Wraith and soon the new allies are working side-by-side. With the help of a Wraith scientist Beckett and Zelenka struggle to weaponize the retrovirus while McKay coordinates with the hive's crew to practice bypassing a hive ship's defenses. The Wraith however make everyone uneasy. Worse their first attempt to target another ship with the new weapon ends in disaster: Their enemies discover the canisters of the retrovirus too soon and open fire. Michael's hive ship and the Daedalus barely escape intact. The imperious Queen of Michael's hive now threatens to reveal Atlantis's existence to all the Wraith if the humans won't design a reliable delivery system for the weapon. McKay frustrated demands that she help by allowing him free access to every last piece of information about Wraith ships. To his astonishment she agrees downloading a virtual encyclopedia of technical specs to Atlantis's computers. Zelenka delves into this goldmine of strategic intelligence while McKay--escorted by Ronon--explores the hive itself and discovers a perfect delivery point for the retrovirus in the atmospheric system. With that they're ready to attempt a second attack: The Daedalus will beam the canister onto another enemy hive. McKay and Ronon will observe from Michael's ship. Sheppard will observe from the Daedalus. But soon after the mission is underway Zelenka discovers that the electronic Wraith encyclopedia was infected with a virus of its own--and now that virus is loose in Atlantis's computers. It's too late to warn the Daedalus which drops out of hyperspace to find itself trapped under a ferocious bombardment from two hives--the enemy vessel and Michael's ship. The alliance was nothing but a ruse; the real plans of the Wraith are far more sinister. Far from giving up on finding Earth they've just tricked the Atlantis team into giving them exactly the information they need to get there.

After their temporary alliance with the Wraith backfires the Atlantis team must find a way to stop two Wraith hive ships that are headed for Earth. Weir (Torri Higginson) orders Colonel Caldwell (Mitch Pileggi) to attack the Hive ships using the Daedalus and the Orion before she is ordered to return to Earth to account for her team's failures. Sheppard (Joe Flanigan) who was able to survive by latching his F-302 to the hull of a Wraith ship is forced to rely on a now ostracized Michael (Connor Trinneer) to help him save McKay (David Hewlett) and Ronon (Jason Momoa) who are being held prisoner by the Wraith. Ronon and McKay are able to free themselves from their cocoon prisons with a plan to sabotage the ship in a last act of heroism. All plans collide as the Daedalus and Orion engage the Hive ships while Sheppard McKay and Ronon are still aboard.

Having successfully used the Wraith retrovirus to turn an entire hive ship of Wraith into humans the team returns to Atlantis with their prisoners in stasis. Weir (Torri Higginson) continues to defend her leadership in the face of an independent review being conducted by IOA member Richard Woolsey (Robert Picardo). Examining the hive ship that the team hijacked in an attempt to restore it to full working condition McKay (David Hewlett) discovers that the Wraith prisoners cannot continue to be held in stasis indefinitely. The team decides the best thing to do is to set them free on a planet under the guise that they were exposed to a viral outbreak. Sheppard (Joe Flanigan) and Dr. Beckett (Paul McGillion) remain on the planet to manage the human-form Wraith including a re-humanized Michael (Connor Trinneer). But when they discover a Wraith ship approaching the planet the team must act fast to keep the existence of Atlantis a secret.

Exploring a village the team is suddenly attacked and taken prisoner. It turns out that Ronon (Jason Momoa) had visited the planet before and unknowingly lured the Wraith there. The Wraith then made a pact with the villagers that if they capture Ronon and contact them the village will be spared from any future culling. On Ronon's request the villagers set Sheppard (Joe Flanigan) and Teyla (Rachel Luttrel) free who then quickly mobilize a strike force to return to the planet and save Ronon. Upon their return however the team finds the village devastated and Ronon taken. Back in the hands of the Wraith Ronon is again implanted with a homing beacon and set free on his devastated home planet of Sateda to once again be hunted by the Wraith. Ronon recalls the fall of his homeworld where his wife and comrades were killed by the Wraith years ago. After the team determines Ronon has been taken to Sateda they must race to the planet to save him.

While looking for suitable stargates to harvest for their new Intergalactic Bridge the team comes across a small village with a revered leader. To their surprise the village's leader Lucius (Richard Kind) has an obnoxious manner and an utter lack of credibility. On Lucious' request Weir (Torri Higginson) sends Dr. Beckett (Paul McGillion) to determine if any of Lucious' potions are worthy of trade. Though at first put off by Lucius Beckett soon becomes so enamored by his host he disobeys security protocol and brings him to Atlantis. By the time Sheppard (Joe Flanigan) and McKay (David Hewlett) return from another stargate harvesting mission they find the entire base has fallen for Lucius' unctuous charm. Believing foul play is at work McKay discovers that Lucius is using some sort of pheromone to enchant those around him. It becomes clear that unless Sheppard can remove the now entrenched and protected Lucius from Atlantis there will be no stopping his charming coup d'etat.

Scouring the Atlantian database Dr. Rodney McKay (David Hewlett) discovers a reference to an abandoned Ancient testing site. Investigating the site the team discovers a vast metropolis supporting millions of Ancients. Eager to create an alliance with such an advanced society Weir (Torri Higginson) is shocked when their leader Oberoth (David Ogden Stiers) refuses the offer. Seeing no way to appeal to their humanity to help save the Pegasus galaxy from the Wraith Weir and the team head back to Atlantis. However before they are able to leave the team is ambushed and taken prisoner by Oberoth and his guards. The team is then subjected to a mind probe by what they now discover are actually replicators in the form of Ancients. Having created the replicators as a weapon against the Wraith the Ancients feared they were losing control of their creation. But the Ancients' attempts to destroy the replicators failed. Now the surviving replicators are divided - some wish to mimic their creators and seek ascension. Others including Oberoth want nothing more than the destruction of Atlantis as revenge for the Ancients' betrayal. Now the team must find a way to free themselves and stop the replicators from reaching Atlantis.

Waking up in a psychiatric hospital outside of Washington D.C. Dr. Elizabeth Weir (Torri Higginson) is shocked to discover that her entire experience in Atlantis over the last two years was solely a figment of her imagination. Through the help of her psychiatrist Dr. Fletcher (Alan Ruck) she learns that a car accident that killed her fiance left her in a near catatonic state and suffering from delusional psychosis. Forced to come to terms with this new reality Weir is visited by her mother and General Jack O'Neill (Richard Dean Anderson) who assures her that he has never heard of a Stargate program let alone the lost city of Atlantis. Yet as she starts to pick up the pieces of her life she continues to have unsettling visions warning her that she must return to Atlantis. Back on Atlantis the team holds vigil for the comatose Weir who in reality has been infected by replicator nanites that are quickly taking over her body and mind. Even with the medical expertise of Dr. Carson Beckett (Paul McGillion) and the emotional support of Lt. Colonel John Sheppard (Joe Flanigan) it is ultimately up to Dr. Weir to save herself and find a way back to the real world.

Summoned to a planet by a communication code they had previously given their Genii allies the team is ambushed by Kolya (Robert Davi) who has now created his own faction of Genii after being forced from the inner circle of the Genii leadership. While the rest of the team manages to escape Sheppard (Joe Flanigan) is taken prisoner. Unable to track down Sheppard on their own the team reluctantly contacts the Genii's new leader Ladon Radim. But they have no way of knowing if Ladon is involved in the kidnapping. When Kolya finally contacts Atlantis however he offers to free Sheppard but only if the Atlantis team turns over Ladon who Kolya begrudges for becoming the new Genii leader. And until his demands are met Kolya intends to drain Sheppard's life by allowing a captured wraith to feed on him. Sheppard's life is slowly drained in successive video taped feeding sessions while Weir struggles with the decision of whether or not to meet Kolya's demands. Meanwhile Sheppard forms a bond with his cellmate who is also a prisoner of Kolya. With a rescue unlikely and his time running out Sheppard forms an unlikely alliance to attempt an escape.

Rodney McKay (David Hewlett) is called back to earth to convince his estranged sister Jeannie Miller to assist the Air Force in implementing an important mathematical proof that has application to one of McKay's experiments. Having not seen her in four years McKay finds it difficult to pry Jeannie away from her family so he has no choice but to disclose the existence of the Stargate program to her. McKay and Jeannie travel to Atlantis and begin the experiment which is intended to generate limitless energy by bridging parallel universes. The experiment is initially successful until a Rodney McKay from the parallel universe appears in the experiment's containment chamber asking the team to shut down the experiment to avoid damaging his universe. And this Rodney McKay preferring to be called Rod is the polar opposite of our McKay with charisma courage and humility in spades. Rod forms an instant bond with Jeannie and the other members of the Atlantis team causing McKay to become instantly jealous. While at first believing the crisis to be averted the team soon realizes that shutting down the experiment from their end won't prevent Rod's universe from being destroyed. And what's worse people in Rod's universe have a plan to save their own universe at the expense of ours. Now Jeannie McKay and Rod must find a way to save both universes and may have to make certain sacrifices in the process.

When a team fails to check in with Atlantis while on a mission exploring an anomalous energy spike Sheppard's team must go in search of the missing men. Arriving on the planet the team immediately discovers the bodies of many dead Genii soldiers. Stranger yet is the fact that they appear to have all killed each other. Still in search of their missing men McKay (David Hewlett) follows the energy readings leading the team to a bunker housing an abandoned wraith experiment designed to manipulate the minds of their prey. Something has gone wrong however and the device now surging out of control is causing disturbing hallucinations. Discovering the bodies of the missing Atlantis team it becomes clear that they fell victim to the hallucinations and killed each other. Now with Ronon (Jason Momoa) chasing after wraith that aren't there and Sheppard (Joe Flanigan) believing he's trapped back in horrible flashback to his time in Afghanistan it's a race for McKay to disable the device before the team all kill one another.

While testing the new McKay-Carter intergalactic gate bridge the Daedalus detects an Ancient Atlantian warship traveling at just below light speed and heading towards Earth. Damaged in battle during the war with the Wraith the Ancients aboard this ship fled the Pegasus galaxy and have spent thousands of years in stasis. Back on Atlantis the now awoken Ancients meet with General O'Neill (Richard Dean Anderson) and Richard Woolsey (Robert Picardo). They thank the Stargate team for taking care of the city in their absence but ask them to vacate Atlantis immediately. While Ronon and Teyla stay in the Pegasus galaxy the remaining team members struggle to resume their lives on Earth. Sheppard (Joe Flannigan) doesn't gel with his new SG team McKay (David Hewlett) is bored in his Area 51 lab and Weir (Torri Higginson) has trouble finding meaning in a life after Atlantis. However the SGC soon learns that the Replicators have overtaken Atlantis as McKay had previously enabled the Replicators to re-write their own base code to override a safeguard preventing them from killing the Ancients that made them. Now with O'Neill and Woosley trapped in Atlantis and General Landry (Beau Bridges) intent on protecting Earth by sending nuclear weapons through the gate to destroy Atlantis the team must figure out a way to save O'Neill Woolsey and Atlantis itself.

Major General Jack O'Neill's mission to defend Atlantis fails as he and Richard Woolsey are taken prisoner during an Asuran assault on the city. Sheppard's team Dr. Weir and Dr. Carson steal a Jumper from Stargate Command on Earth and come back to Pegasus galaxy with a plan to retake Atlantis.

Teyla (Rachel Luttrell) begins to see apparitions of ancients in distress and believes they are the ghosts of the Ancients recently massacred by the Replicators. Meanwhile Rodney McKay (David Hewlett) believes he's found the whale that saved him a year ago while trapped in a submerged puddle jumper. But while taking a jumper out with Col. John Sheppard (Joe Flannigan) to investigate his old friend they discover the whale is not alone but is one of dozens of its kind all headed directly to Atlantis. With their high pitched sonar the whales begin to painfully effect the inhabitants of Atlantis. Teyla whose visions are now being shared by others believes it's this threat the whales pose that the ancients are trying to warn them about. Not till McKay discovers one of the Ancient's labs created to study and communicate with the whales does he realize that the whales are creating the apparitions. The visions are meant to warn Atlantis of a large scale coronal mass ejection from a nearby sun strong enough to destroy the city and all life on the planet. Without the necessary power the Ancients used to protect the planet from a similar disaster fifteen thousand years ago Sheppard improvises a plan to use their only ZPM aboard the Daedalus to block the blast above the ejection point. The plan however requires the Daedalus to fly almost directly into the sun.

Sheppard (Joe Flanigan) and his team hear of a great warrior with stories of defeating both the Genii and the wraith and decide to seek him out in hopes of making a powerful new ally. But when they learn this great warrior is none other than Lucius (Richard Kind) they believe he's up to his old tricks again. Claiming he is in fact now invincible his demonstration of his power reveals he's actually found one of the Ancient's personal shields. Ready to leave him about his ways the team is ambushed by angry raiders and must rely on the invincible Lucius to save them. Sheppard not willing to believe all is as it seems follows Lucius to learn he is actually in cohorts with the raiders. Deciding to blow the whistle on Lucius' scam the danger suddenly becomes all too real when Kolya (Robert Davi) shows up demanding the Atlantis team be handed over to him. With Lucius used as bait the whole team except Sheppard is taken prisoner. With no way of reaching Atlantis for re-enforcement it's up to Sheppard to save the team before Kolya begins his promised executions.

Trying to preserve power by turning off all the non-essential systems the Ancients recently activated before being killed by the replicators Rodney McKay (David Hewlett) mistakenly is hit by an energy beam from a mysterious device. His worst fears are quickly laid to rest when Dr. Beckett (Paul McGillion) gives him a clean bill of health and returns him to active duty. Not long after the incident Rodney begins to display advanced powers such as amplified senses and telekinesis. Unable to ignore his powers Rodney and Zelenka (David Nykl) discover the machine that zapped him actually accelerated his evolution. Basking in his new found super power exponentially growing intelligence and equally bloated ego the team struggles to deal with the new Rodney. But envy turns to concern when Weir uncovers the true nature of the ancient device. Designed to accelerate a person's evolution it was designed to speed up the process of ascension. However without being able to achieve the same advancement in mental state the machine killed most of the ancients that ever tried to use it. Death looming as he continues to physically evolve Rodney tries to crack the secret of ascension in quantified terms. With no success in site he resolves to use his final days making peace with his colleagues and friends even if they aren't ready to give up on him just yet.

Major Lorne (Kavan Smith) discovers a planet with dozens of satellites in geosynchronous orbit. However inhabitants on this plante are no further advanced than being themselves in a renaissance period and even stranger he discovers a flag baring Rodney McKay's (David Hewlett) likeness. Informing Rodney and Lt. Col. Sheppard (Joe Flanigan) of this the team realize a game they had found years earlier on Atlantis might actually be much more than just a game. Realizing that an ancient sociological simulation actually sent orders to two competing city-states Weir (Torri Higginson) demands that McKay and Sheppard set things between the once peaceful neighbors right. Meeting each of the cities representatives Nola (Laura Harris) and Baden (David Dayan Fisher) the two men find that their dipolatic mission may be much more difficult than they thought. Before they have time to usher in a new peace the two cities take matters into their own hands and embark on a world war with much more advanced weapons than the Atlantis team were aware of. The two bickering friends must find a way to stop it or be responsible for what could be the destruction of two civilizations.

Investigating what appears to be an abandoned space station inside a hollowed out moon Rodney McKay (David Hewlett) mistakenly brings one of it's scientists out of stasis. The scientist Henrick (Joris Jarsky) explains to the team that the base was the last effort by his people to avoid the repeated culling they've endured for generations at the hands of the Wraith. Using the Wraith stasis technology they modified a chamber to hold a large number of their people for thousands of years in the hope the wraith would find their empty planet and believe they had disappeared. But when Henrick discovers only half the number of stasis pods are present he extracts his people's leader Jamus (Kenneth Welsh) to explain. Learning that the Wraith attack had come sooner than expected Jamus sacrificed the last pod to conceal the whereabouts of the space station from the Wraith. Unable to deal with the loss of his wife and children who were in the lost pod Henrick tries to vent the space station by igniting the remaining spaceships rockets. But when Henrick discovers only half the number of stasis pods are present he extracts his people's leader Jamus (Kenneth Welsh) to explain. Learning that the Wraith attack had come sooner than expected Jamus sacrificed the last pod to conceal the whereabouts of the space station from the Wraith. Unable to deal with the loss of his wife and children who were in the lost pod Henrick tries to vent the space station by igniting the remaining spaceships rockets.

With the entire city ordered to take a personal day the team does their best to unwind and enjoy their leisure time. Without warning a mysterious explosion rips through the city killing and injuring unsuspecting citizens. Dr. Rodney McKay (David Hewlett) and Dr. Carson Beckett (Paul McGillion) arrive on the scene to find Teyla (Rachel Luttrell) critically injured by shrapnel from the explosion. Unable to find explosive residue the only leads they have to go on are eyewitness accounts saying one of the base-scientists just suddenly exploded. McKay realizing the scientist in question is one of his own quickly puts the pieces together to learn that the incident is likely the cause of an Ancient device mistakenly activated days earlier by two of his scientists. The device which is actually a type of weapon infects nearby organisms with a tumor-like explosive that detonate after reaching critical mass. Knowing that the other scientist is still somewhere on the base the race is on to track down the man who is literally a walking time bomb before he explodes and injures more people.

Deep underwater the team scours the ocean floor looking for a mobile geothermal drilling station the ancients left dormant in hopes of unleashing near limitless power from beneath the planet's surface. The team finds the drilling rig and cautiously explores the station the Ancients chose to abandon. Using her gift Teyla (Rachel Luttrell) thinks she senses the presence of a Wraith but repeated life scans by McKay (David Hewlett) show nothing out of the ordinary. Weir (Torri Higginson) believing it's just the pressure affecting Teyla has the team press on to explore the station. Without warning Teyla suddenly attacks Ronon (Jason Momoa) and sets up a series of force fields to block the team from the jumper. But when Col. Sheppard (Joe Flanigan) corners her she has no memory of doing anything wrong. Using Teyla successfully as a puppet a Wraith Queen now aboard the station attacks two scientists to lure Sheppard to the jumper in hopes of using him to fly her to the surface. Unable to overcome the power of the Queen Sheppard is helpless and saved only by Ronon mistakenly blasting the jumper windows sending a wall of ocean water onto Sheppard and the Queen. With the Wraith Queen now restrained and sedated Teyla uses her gift to learn that the Queen was part of the first wave of attacks on Atlantis. Her cruiser was shot down sending it plummeting to the ocean depths. Surviving only by feeding on her crew she woke between centuries in the hope of a rescue that never came. Sensing Teyla's presence as they descended she awoke knowing the ship she sought had finally come. Wanting to either escape her watery prison or die the queen activates a self-destruct on her ship. If the team is unable to stop the resulting explosion over the thin layer of crust the drilling station sits on it would ignite a catastrophic chain reaction.

After helping relocate the Taranans the Atlantis team realizes they haven't heard from the village in an unusually long period of time. Wondering what happened to them Weir (Torri Higgenson) sends Sheppard (Joe Flanigan) and his team to go investigate their village. Once there it appears the Taranans have just abandoned their village until Rodney McKay (David Hewlett) detects life signs well beneath the surface in the remnants of the previous village's underground industrial complex. Searching the dark winding corridors of the abandoned tunnels the team comes upon some sort of cocoon as well as a lab that appears to have been used for Wraith experiments. Discovering the bodies of several Taranans who appeared to have been fed on by the Iratus bug the team has little time to piece the puzzle together before they themselves are attacked by a large insect-like monster. Their weapons are useless against the creature's exoskeleton. Ronon is barely able to fend it off by cutting off one of its arms. Radioing for backup the support team manages to make it through the gate just moments before a wraith dart scoops them up. Back in the tunnels Teyla (Rachel Luttrell) becomes separated from the team and taken prisoner by the scientist who created the beasts Michael (Connor Trinneer). He explains that after being treated as an outcast by his own people unable to live as a wraith or a human he decided to create an army of his own. Using what he learned from Dr. Beckett's retro-virus and through experiments of his own he's been able to build a super bug. Having used the entire Taranan village as food for his experiments he plans to use Teyla to the same end.

With the arrival of the Apollo to Atlantis comes intel that the Replicators appear to be building a large armada to directly attack earth. Planning to strike first Col. Ellis with the aid of the Atlantis team launches a surgical strike nuking the entire armada. Believing that all imminent danger has been avoided the team is shocked when a satellite housing a stargate takes up geosynchronous orbit above Atlantis. Unable to destroy the Stargate it opens transmitting a powerful energy beam impacting Atlantis' shields. Being powered from the point of origin neither the beam nor the satellite's shields show any vulnerability to the Apollo or Atlantis. Without any way of avoiding the beam as it quickly drains the ZPM powering the shields Rodney McKay opts to sink the city as the ancients did millennia ago using the water to dissipate the beams strength. But when the sinking of the city doesn't have the desired effects it appears it's only a matter of time before the shields fail. With the stargate active in such close proximity it renders the city's gate inactive. Their only hope is to use what energy the ZPM has left along with strategic cover by an asteroid to hopefully fly the city into hyperspace before the shields collapse. But when the asteroid fails to hold allowing the beam to cut through to the city it seems unlikely Atlantis will make it off the surface in one piece.

When Rodney McKay (David Hewlett) realizes Atlantis has started shutting down artificial gravity and collapsing protective shields to compensate for a damaged power system he turns off all non-essential systems. But when the problem persists McKay is forced to collapse the shield to the point where it is only protecting Atlantis' main tower leaving the rest of the city exposed to space.With the protective shields down and an asteroid belt fast approaching Lt. Col. Sheppard (Joe Flanigan) leads a group of Atlantis personnel on a desperate jumper mission to clear a path for the city. Meanwhile Dr. Keller's (Jewel Staite) attempts to resuscitate a comatose Elizabeth Weir (Torri Higginson) reveal that her patient has severe brain swelling and will require radical surgery. McKay runs the calculations and realizes there's an even bigger problem: in just 28 hours the city's shields will fail completely and all of Atlantis' inhabitants will succumb the vacuum of space.

Lt. Col. Sheppard (Joe Flanigan) leads his team on a daring raid on the Replicator home world in a bid to secure a ZPM that will save Atlantis. The key to their operation is none other than Dr. Elizabeth Weir (Torri Higginson). Directed by Weir and McKay (David Hewlett) from the jumper Sheppard and Ronon (Jason Momoa) head deep into the Replicator city to acquire the sought after prize. But a surprising revelation concerning a long-dormant Replicator sub-routine changes the plan forcing Sheppard and company to forego their quick escape. When the Replicators become aware of the incursion Sheppard's team must keep them at bay or else abandon the mission and their hope of saving Atlantis. Meanwhile Colonel Carter (Amanda Tapping) aboard the Apollo searches in vain for the missing city.

On an off-world village Ronon (Jason Momoa) and Teyla (Rachel Luttrell) discover a group of warriors from Ronon's homeworld Sateda. These Satedans led by Tyre (Mark Dacascos) have a plan to infiltrate a Wraith weapons facility but need the Atlanteans help to do it. Meanwhile Col. Samantha Carter (Amanda Tapping) arrives on Atlantis as the new leader and her first task is to execute new security protocols that leave Ronon feeling alienated and considering leaving Atlantis for good. Once inside the Wraith weapons facility the two teams split up and Sheppard (Joe Flanigan) and his team come under fire from the Wraith. Ronon escapes but Sheppard and company are captured. The Wraith force McKay (David Hewlett) to make changes to the Replicator base code using an actual Replicator the Wraith have imprisoned in the facility. Ronon and Carter mount a rescue operation and in the end Ronon learns the truth about his old friends' new loyalties.

While Lt. Col. Sheppard (Joe Flanigan) and the team are out exploring a jungle planet they discover a glowing crystalline growth. Compelled to touch the strange crystal Sheppard becomes host to an alien entity. Once on Atlantis the entity begins to move from person to person through the power of touch. Teyla (Rachel Luttrell) is the first to experience a nightmare involving Sheppard. The chain reaction continues when she infects Dr. Keller (Jewel Staite) who succumbs to a different but equally terrifying dream. When Lorne (Kavan Smith) appears to have a psychotic breakdown the team urgently attempts to trace the problem to its source. When Rodney McKay (David Hewlett) becomes the latest host the team links Sheppard to McKay's brain where Sheppard ultimately faces off against the malevolent entity that has assumed his form.

Ambushed and imprisoned aboard a rogue human-run ship Lt. Col. Sheppard (Joe Flanigan) is threatened with death by its attractive female commander Larrin (Jill Wagner) unless he helps her reactivate a dormant Lantean spaceship. A nomadic group of travelers live on this rundown vessel part of a greater armada and their need for new ships has become critical. As soon as Sheppard steps aboard he discovers that the Lantean ship abandoned after an attack by the Wraith is now emitting deadly radiation. Unbeknownst to Larrin Sheppard manages to send out a sub-space distress signal - but the signal attracts a Wraith cruiser. As the team searches for him Sheppard's resourcefulness is put to the test as he tries to stay alive with or without Larrin's help.

Plant samples brought back from a new planet introduce an amnesia-inducing virus that strikes everyone in the city except Teyla (Rachel Luttrell) and Ronon (Jason Momoa) who appear to be immune. Carter (Amanda Tapping) orders the Gate's control crystal removed to stop the disease from spreading to other planets while Major Lorne (Kavan Smith) and his soldiers are given orders to control the Atlantis population with stun guns. The team discovers that a cure might be available among the plants on the mainland so Ronon and Sheppard (Joe Flanigan) whose memory is also fading set off to obtain it. Meanwhile McKay (David Hewlett) works on a widespread distribution method but is unable to complete it before he too succumbs to the virus. When McKay wakes up he is strapped to his desk in front of his console with no idea who he is or what is going on. Following instructions from a video he recorded earlier McKay frees himself and sets out to find Teyla (Rachel Luttrell) the key to unlocking this mystery.

Teyla (Rachel Luttrell) is shocked to find the Athosian settlement on New Athos completely deserted when she and Dr. Keller (Jewel Staite) arrive for a visit. Upon encountering the menacing Bola Kai a fierce warrior tribe the two women flee for their lives into the surrounding forest. Virtually weaponless and slowed by Keller who has injured her ankle the pair must avoid capture by the Bola Kai until their failure to return alerts Atlantis to send a search party. Keller and Teyla find a bound and wounded man named Nabel (Johann Hels) who claims that Teyla's people were culled by the Wraith. Ultimately the three are captured and the Bola Kai's tribe leader Omal (Danny Trejo) threatens to kill them unless they betray the location of Atlantis.

With still no trace of the Athosians Teyla (Rachel Luttrell) requests an off-world visit to meet with a seer Davos (Martin Jarvis) who may be able to help her find her people. After convincing even McKay (David Hewlett) the most skeptical of the team of his psychic abilities an ailing Davos travels back to Atlantis to receive medical treatment. While there he has visions of tragic and devastating consequences for Atlantis. Meanwhile the Wraith bring a startling proposal to Lt. Col. Sheppard (Joe Flanigan) along with information that the Replicators are finding new ways to destroy human civilizations throughout the galaxy with devastating results. The only way to stall their attacks may be to collaborate with the Wraith in a dangerous partnership. Adding to the stress on Atlantis is the arrival of Agent Woolsey (Robert Picardo) who has been assigned to observe and review Col. Carter (Amanda Tapping) in her newly appointed position as leader of the city.

After working for countless hours on the Replicator coding Dr. McKay (David Hewlett) reluctantly admits that he needs help with the program. And the only available person who can match - or exceed - his knowledge is his sister Jeanie (Kate Hewlett). After working on the calculations from Earth Jeanie sends her results back to Atlantis and heads to bed. But the calm is broken when her bedroom is stormed by four men wielding MP-5's who tie up her husband and drag Jeanie into the night. When news reaches Atlantis that his sister is missing McKay travels to Earth racked by guilt for involving his sister. He is determined to find her and uncover who is behind the kidnapping. But when McKay also goes missing it's up to Lt. Col. Sheppard (Joe Flanigan) and Ronon (Jason Momoa) to figure out who has stolen the Replicator information... and the only two people who have the knowledge to understand it.

As Dr. Rodney McKay (David Hewlett) struggles to figure out why the stargate has been inoperable for over a week a mysterious probe plunges into the city. A subsequent decryption sweep of the probe offers McKay a shocking glimpse of nanite code before his diagnostic program crashes and all the data is lost. Meanwhile Lt. Col. Sheppard (Joe Flanigan) Teyla (Rachel Luttrell) and Ronan (Jason Momoa) have noticed that the some of the crew are behaving oddly. The mystery deepens still further when a former member of the expedition is discovered lying unconscious in a hidden room. Convinced that the replicators have finally found their location the team grapples with these implications unaware that their problems may very well be insurmountable.

The Replicators remain undeterred in their effort to wipe out the Wraith's human food supplies but the Atlantis team is now armed with the means to track their ships. With time in short supply Sheppard (Joe Flanigan) Teyla (Rachel Luttrell) and Ronan (Jason Momoa) rush to evacuate those human settlements which lie in the path of the advancing Replicator forces. Meanwhile both Colonel Caldwell (Mitch Pileggi) commander of the Daedalus and Colonel Ellis (Michael Beach) commander of the Apollo arrive from Earth. Each is in possession of Asgard based weaponry ready to confront an armada of Replicator ships. But Dr. McKay (David Hewlett) is not convinced that this is the best offensive and in partnership with a wraith scientist struggles to create a program that will effectively shut down the replicators for good. But the team's best laid plans are fraught with hurdles further fuelled by an unexpected appearance from Larrin (Jill Wagner) the leader of a race of space travelers not unknown to Sheppard.

High above the Replicator homeworld a provisional alliance wages an all-out assault on the Replicator fleet. As the battle wages a group of wraith execute a last-minute plot to retrieve a ZPM from the planet's surface. Weeks later the Atlantis long-range sensors detect the signal of a subspace tracking device familiar to Dr. McKay. The team follows to signal to a damaged hive ship drifting in space. Amidst the ship's records they discover references to a secret wraith base...

A nervous Dr. McKay (David Hewlett) arrives in the botany lab prepared to pop the question and finally ask Katie to marry him when an alarm sounds throughout the city. A quarantine lockdown goes into effect trapping them in the lab. McKay suspects that a highly infectious disease has triggered the city's automatic self-protection system.

While re-visiting an off-world trading partner Lt. Colonel Sheppard (Joe Flanigan) and Dr. McKay (David Hewlett) receive high praise from the beautiful princesses Mardola (Crystal Lowe) and Flora (Anna Van Hooft) who express their undying gratitude for the trade medical assistance and protection Atlantis has provided for the past several years. The princesses beg a further favor asking Sheppard and McKay to accompany their sister Harmony (Jodelle Ferland) designated successor to the throne to the ruins of the Temple of Laros a mandatory rite of passage. Reluctant to jeopardize their otherwise untroubled alliance and anticipating that the third sister will be equally beguiling Sheppard and McKay agree to escort Harmony on a journey promised to take no longer than a day. Their chivalry is challenged upon meeting Harmony a thirteen year old child with high expectations of her protectors. Disheartened Sheppard and McKay nonetheless proceed with their mission unaware that she has enemies and character flaws yet to be dealt with.

When Lt. Colonel John Sheppard (Joe Flanigan) is informed that his father has passed away he packs a few things and accompanied by Ronan (Jason Momoa) heads back to Earth to attend the funeral. There Ronan gains some insights to his friend's past - Sheppard's troubled relationship with his father and brother as well as his ex-wife Nancy a director with Homeland Security. Before long they are approached by a woman Ava Dixon who claims to know about a covert project involving nanite programming. Sheppard's worst fears are realized when she leads them to a high tech lab and reveals that she and her partner have been successful in creating a human form Replicator - a Replicator now loose somewhere in the city who must be recaptured at all cost.

Col. Samantha Carter (Amanda Tapping) joins Dr. McKay (David Hewlett) and Dr. Keller (Jewel Staite) on a mission to convince the inhabitants of an off-world village rocked by frequent tremors to move to a more stable part of the continent. But en route to the village Dr. McKay plunges into a sinkhole falling twenty feet to the bottom of a large subterranean chamber. Crawling to the edge of the rupture Carter and Dr. Keller are relieved to see that McKay is unhurt. Suddenly they feel the ground beneath them give way and they too drop out of sight. Realizing that they have fallen into a section of an old Genii mining facility they begin to search for a way out. But every attempt to escape the confines of the chamber seems to put them in further jeopardy underscored by the constant tremors that shake their prison with ever greater force.

Mr. Coolidge is the newest member of the IOA and openly distrustful of alien participation in any facet of the Stargate program. Despite his bias the IOA has entrusted him with interviewing Teyla Emmagan (Rachel Luttrell) and Ronan Dex (Jason Momoa) about their suitability to continue as members of the Atlantis expedition. This does not bode well for Ronan who is next on the list to travel to Earth for questioning. Colonel Carter (Amanda Tapping) concerned that Ronan's temper will explode under intense cross-examination asks an old friend to travel to Atlantis to serve as his mentor - Teal'c of the Jaffa. But Ronan insulted by the implication that he can't handle himself makes no effort to befriend Teal'c and their stay on the Midway station en route to Earth does little to improve the situation. Unbeknownst to anyone a plan by the Wraith to invade the Midway station is about to be initiated and an interview with Mr. Coolidge will be the very least of their problems.

Dr. Keller (Jewel Staite) is perplexed by a mysterious new sickness that has affected a number of planets in the Pegasus Galaxy and threatens to kill hundreds of thousands of people. Further study reveals that it is not a contagion but a human engineered protein designed to kill a feeding wraith. Col. Carter (Amanda Tapping) and Dr. Keller realize that someone is intentionally infecting the Wraith's food supplies with no concern for the thousands of human carriers who are dying in the process. Meanwhile Teyla (Rachel Luttrell) shares with Dr. McKay (David Hewlett) a vision she had in which Kanaan the father of her child was trying to send her a message that he is still alive. Now more determined than ever to find him and the other missing Athosians she convinces Sheppard (Joe Flanigan) to travel with her to a trading settlement in search for answers. What they find there leads them to startling discovery that no one could have anticipated.

Everyone on Atlantis is surprised to learn that a friend once thought dead is miraculously back among them. A captive Teyla (Rachel Luttrell) meanwhile is re-united with her missing fellow Athosians who have also been interned at one of Michael's secret facilities. Ever hopeful that Sheppard (Joe Flanigan) will be able to mount a rescue she begins to formulate a plan to ensure their escape if he is able to find them in time.

Disheartened by another unsuccessful search for Teyla Lt. Colonel Sheppard (Joe Flanigan) returns home to Atlantis and immediately senses that something is not right. Further investigation reveals that not only has the city been completely abandoned its systems are all dead and instead of ocean is now surrounded by rolling sand dunes as far as the eye can see. A significantly older looking McKay appears - a hologram with devastating news to relay. A freak anomaly has sent Sheppard over forty thousand years into the future and everyone he has ever known is long dead. But McKay has a risky plan to return Sheppard to the past and reverse a future that went horribly wrong.

An injured Sheppard is trapped alongside Ronon beneath the rubble of Michael's collapsed compound. Trapped in another debris pocket McKay and Lorne realize that a subspace burst has already reached Michael. Light years away Michael's flagship Wraith Cruiser hurtles towards the compound. Imprisoned onboard a pregnant Teyla begs Kanann the father of her baby to help save her. Carter leads a rescue mission to the planet. Her team succeeds in digging up McKay and Lorne but Ronon and a rapidly deteriorating Sheppard are buried far deeper in the rubble. With Michael and his hybrids on their way back to deal with intruders and the Daedalus already enroute the question becomes: Who will reach them first?

When Dr. Keller fails to report for her morning shift concerned team members investigate and are shocked by what they discover: Jennifer unconscious in her quarters - a mysterious web of tendrils attached to her body. Suspecting her condition may be linked to her research into the wraith data recovered from Michael's lab the team makes the decision to bring Beckett out of stasis. The beloved doctor leads the medical investigation while Sheppard and co. are quarantined under suspicion that they may have been exposed to the same virus that has affected Keller. As Beckett struggles to find a solution the alien organism grows creeping out into the adjoining corridors toward the main power grid. With Atlantis itself now under threat Woolsey is ultimately faced with a decision that could cost Keller her life.

Ronon is ambushed during an off-world mission and awakens much later a prisoner of his former friend Tyre. The fellow Satedan it turns out has fallen on hard times since they last crossed paths. Abandoned by the wraith he once served he is undergoing a physiological and psychological withdrawal from the reverse-feeding process once granted to him as a wraith worshiper. But he believes he has come up with a way to win back the respect of his former masters: by delivering them Ronon. Intent on turning their defiant captive the wraith begin their process of reverse-feeding - stealing Ronon's life bringing him to the brink of death then restoring his youth. Again and again and again. A tip meanwhile leads the team to an abandoned village. But Ronon and the wraith are long gone and the only remnant of their former presence is a seriously injured Tyre who may be their only hope of rescuing their friend.

When a mysterious duplicate Daedalus appears in orbit over Atlantis the team is dispatched to investigate. Once aboard the deserted and severely damaged ship the team discovers an ominous video message from the former captain. But before they can make sense of the situation the ship is propelled into an alternate reality. As McKay tries to figure out what is going on the ship continues to jump through various alternate realities encountering an alien armada and the blistering heat of an expanding sun. Worse - the team realizes that if they don't find a way back to their reality soon they risk being lost forever.

Returning from an exploratory mission the team is mystified when an arc of blue energy causes the puddle jumper's primary systems to shut down slamming them into an active stargate. They narrowly make it home only to be greeted by similar erratic anomalies within the city itself. Soon nearly every system in Atlantis is affected by ominous power disruptions. Suddenly a puzzling message appears on McKay's computer screen. Its author claims to be a former friend long thought dead. Now an incorporeal presence she begs Rodney to utilize the Ancient's technology to build her a new body. Highly skeptical the Atlantis team is faced with an impossible decision. To create the means to release an entity who may or may not be a friend or stand by as it systematically destroys the city's technological infrastructure.

En route to check on a missing research team Lt. Col. Sheppard Dr. McKay Teyla and Ronan emerge from the stargate to find themselves swimming atop a flooded valley. With only the apex of the gate accessible above the waterline they cling to it - soaked and bitterly cold - until a puddle jumper can make it through to rescue them. But during the flight back to Atlantis McKay inexplicably falls ill and in the days that follow his condition declines further. Dr. Keller discovers a parasitic organism in his brain that cannot be surgically removed. As a result his ability to function continues to deteriorate to the point where he has virtually no recollection of who he is or what he is capable of. Soon his emotions and memories have regressed to those of a young boy and fearing that he will not pull through the doctor summons Jeannie McKay's sister to say her final goodbyes. But it's too late. Rodney no longer recognizes her or any of his friends. However Ronan has a plan albeit a very risky one. He tells Jeannie of a place - a shrine located on the planet Talus - that would grant Rodney one day to be himself again before he dies.

Dr. Beckett is asked to delay his departure from Atlantis when word comes that Major Anne Teldy and her away team Sgt. Dusty Mehra Cpt. Alicia Vega and Dr. Alison Porter have stumbled onto one of Michael's labs inside an extensive underground catacomb. He and Lt. Col. Sheppard gate to Teldy's location where further investigation reveals an abandoned laboratory containing numerous stasis pods. While Dr. Beckett and Dr. Porter stay behind to sift through the research data that Michael left behind Sheppard and Teldy's team set out to explore a nearby village. Beckett and Porter conclude that Michael was experimenting on the genetic characteristics of several different life forms. Meanwhile Sheppard and his team arrive at the village to find it abandoned. Yet chilling walls of fog and flashes of movement within it suggest that they are not alone.

Keller and the Atlantis team meet with the wraith Todd to deliver a startling proposition. Aided by her studies of Michael's retrieved data Keller believes she has found the means by which to cure the Wraith of their need to feed on humans. All she requires are some wraith willing to act as test subjects for this breakthrough treatment. Todd is intrigued but insists that they must first win the support of the Primary - the supreme Wraith Queen in the alliance. But to do so Teyla must go undercover with nothing to rely on but her wraith DNA and an ally with a hidden agenda.

McKay and Ronan each unaware of the other's motive volunteer to assist Dr. Jennifer Keller with a medical follow-up away from Atlantis. But once in the settlement a nervous child patient prompts Keller to ask Ronan and McKay to wait for her in the local tavern while she finishes her treatment. Later when the pair return they are surprised to learn that she left sometime ago. An exhaustive search of the village turns up no sign of her. But a set of footprints in the dirt just past the village confirms Ronan's mounting suspicion that Keller has been kidnapped. Ronan wasting no time begins to track her abductor while McKay runs back to the stargate to radio for assistance. But just as he reaches the DHD four Hunter Wraith come through the gate and fan out in separate directions. Ronan knowing full well that these Wraith exist to chase Runners suspects there is a connection to Dr. Keller's disappearance. And he knows he must draw on his uncommon skills as a former Runner if he is to save her.

Stargate SG-1's Dr. Daniel Jackson travels to Atlantis when his research suggests that a rebellious Ancient scientist named Janus may have hidden a secret lab somewhere within the city. Hoping to find it and possibly a significant portion of his unauthorized research Jackson enlists Dr. McKay's help. An obscure log entry leads them to a cloaked lab where they unwittingly activate a signal on a distant planet. Hours later the city is paid a visit by a group of mysterious aliens. Meanwhile Woolsey along with Dr. Keller and Ronan have joined Colonel Caldwell on board the Daedalus leaving Sheppard in charge of Atlantis. They welcome Todd and his delegation to the ship to discuss testing Keller's gene therapy on live Wraith subjects. But events take a turn for the worse when Todd suspecting them of betrayal takes control of the Daedalus.

Dr. Daniel Jackson and Dr. Rodney McKay have been forced to reactivate the Attero device a machine designed thousands of years ago to annihilate the Wraith. In doing so they discover the reason the device was ultimately abandoned by its Ancient creator - while destroying Wraith ships that attempt to travel through hyperspace the weapon inadvertently causes active stargates to self-destruct. Meanwhile Todd and his troops continue to hold Woolsey Keller Ronan and the Daedalus crew captive convinced that they are behind the resurrection of this deadly technology. Fearing that if Todd succeeds in destroying the device Jackson and McKay will most certainly be killed in the process Sheppard calls on some old allies to help him rescue his friends.

Col. Sheppard and his team locate Dr. Carson Beckett on an alien planet where he is treating a small group of survivors of the Hoffan plague. These patients who escaped a Wraith attack on their home world Balar have found sanctuary and friendship on this alien planet. But that same evening a party of Wraith warriors appears before the village's councilors demanding that the refugees be turned over to them - threatening total annihilation if they refuse. The Balarians aware that they are not only immune but lethal to a wraith feeding fear there is no chance the townspeople will continue to harbor them. And they may be right. Despite Sheppard's best efforts it appears the original residents intend to sacrifice the newcomers in order to save themselves.

Leaders from the human populations of many worlds have formed an official alliance and extend an invitation to Lt. Col. John Sheppard and his team to represent Atlantis at their next meeting. But on arrival the team is immediately detained in a concrete cell and Sheppard is brought before three council members - Kelore of Latira Shiana of the Tribes of Santhal and Dimas of the Free Peoples of Riva - to stand trial for crimes against the indigenous peoples of the Pegasus Galaxy. Richard Woolsey meanwhile receives a visit from Myrus a representative from the new coalition of planets who advises him that Sheppard and the others are being made to answer for the deaths of millions throughout the galaxy. Outraged Woolsey demands that Myrus bring him to his people confident he can take on their defense and secure their freedom. But it quickly becomes clear that even Woolsey's formidable legal and diplomatic skills may not be enough to save the Atlantis expedition from a guilty verdict.

Col. Sheppard and Dr. McKay are enjoying some recreational time on the pier level of the city when Atlantis is plunged into darkness with only the top tier of the central tower unaffected. Struggling to make their way up to the Gate Room on foot more than 70 levels above McKay speculates that someone has taken control of Atlantis by hacking into the city's mainframe. As they close in on the location McKay picks up extreme energy readings. An unusual force field has been established to prevent them from gaining access to both the Gate Room and Control Room. Meanwhile as Teyla checks on her son Torren two dark figures infiltrate her quarters and fire rendering her unconscious. When she comes to she finds herself in Woolsey's office with the baby sleeping nearby. Distraught she moves to reclaim him then realizes she is not alone. Her ultimate nemesis Michael stands before her - and he is bent on revenge.

Woolsey admits to Teyla Ronan and Dr. McKay that he's apprehensive about an upcoming performance evaluation. Later while en route to his quarters he encounters Dr. Vanessa Conrad an engaging scientist recently arrived on the Apollo and finds himself more than a little attracted to her. But she is quickly forgotten when I.O.A. representative Shen Xiaoyi appears and advises him that he's been reassigned to a new position back on Earth. Woolsey is shocked by this news but aided by his new acquaintance elects to fight the I.O.A.'s decision. Col. John Sheppard meanwhile has flown several astrobiologists over to the mainland for a two day research expedition. On his way to make camp he is ambushed and captured by an old foe hellbent on acquiring Sheppard's identification code. Back on Atlantis McKay and Zelenka investigate a mysterious object discovered at the ocean's bottom.

When the Atlantis team is given two weeks of vacation leave Dr. Rodney McKay reluctantly accepts an invitation by his former rival Malcolm Tunney to attend a scientific demonstration that he claims will be the solution to global warming. Feeling bold he asks Dr. Jennifer Keller to accompany him and she accepts. Upon reaching Earth they are flown by private lear jet to a top secret facility in the middle of a desert. Once there McKay is shocked by Tunney's brazen claims that he's invented a device that can cool the Earth by venting excess heat from our space/time into another space/time - an idea McKay had already pursued two years earlier. Despite Rodney's mounting concerns over its safety Tunney activates his new technology dropping the heat contained inside the facility by 10 degrees. But when the device reaches this goal and will not disengage McKay realizes he has to work fast or every one trapped inside the premises will freeze to death within the hour.

A hive ship comes out of hyperspace directly over the city of Atlantis and transmit's a garbled message. Despite missing data McKay is able to make out a reference to Dr. Keller's gene therapy and an urgent request for help. On high alert Col. Sheppard and his team launch a cloaked puddle jumper to investigate. They board the ship to discover the entire crew in stasis and a prerecorded message from their nemesis - Todd. In it he reveals that he and the crew were stricken with a disease - a complication of the gene therapy developed by Dr. Keller which they had tried to self administer. Many died and the rest were put in stasis. Now they need Atlantis's help. After much deliberation Mr. Woolsey gives the go-ahead. Back on the hive ship Dr. Keller struggles with the complexities of Wraith physiology as the other team members begin to notice something very unsettling - the hive ship itself has somehow been impacted by the disease with dire consequences for all on board.

When it's observed that Dr. Jennifer Keller is behaving very strangely Dr. Carson Beckett is asked to examine her. But extensive testing reveals nothing abnormal and they fear she may be suffering from a mysterious psychological disorder. Unbeknownst to them Keller has traded bodies with that of a notorious criminal Neela Casol and finds herself at the mercy of a village magistrate on a distant planet about to be executed for her crimes. McKay's investigation leads him to suspect that Dr. Keller and Neela have switched consciousnesses by means of an Ancient communications tool. In a race against time Sheppard and his team must locate Keller along with the alien device. But they'll need Neela's help to do it.

Police find a desiccated corpse on a desert road outside Las Vegas Nevada the seventh victim of a bizarre serial killer. Detective John Sheppard called in to assist is baffled by these murders. Then a clue traces of radiation found on the bodies leads him to a strange looking man with super human attributes who easily evades capture. Some time later Sheppard is detained and driven to Area 51. There he meets Dr. Rodney McKay who reveals that the suspect is in fact an alien - a wraith - who feeds on human energy. What's more McKay and his team have traveled to Earth from the Pegasus Galaxy by way of a stargate to prevent this wraith from compromising the security of the planet. But so far Sheppard is the only one who's been able to get close to him.

Todd contacts Atlantis and reveals that a Wraith subordinate has managed to acquire several zero point modules that he has used to power a formidable new hive ship. He urges Woolsey to attack and destroy before it becomes a threat to Atlantis. On board the Daedalus Colonel Caldwell Colonel Sheppard and the rest of the team rush to engage the new hive ship. But the ZPM powered vessel proves itself an impressive opponent crippling the Daedalus before making a sudden and inexplicable jump into hyperspace. Puzzled over the Wraith's sudden departure the team picks up a weak subspace signal in Wraith code. McKay is quick to recognize that the communique was sent through subspace from another reality. Once deciphered their worst fears are realized. The Wraith message contains a familiar set of coordinates. The hive ship is on its way to Earth!