With only 24 hours of power left, and unable to use the Stargate, the Atlantis team must once again save the city from certain doom, while Dr. Weir struggles to survive.

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Now on board the Apollo, Carter proposes they cannibalize several key systems in order to extend the range of the sensors. Although that part of the operation is successful, they require numerous hyperspace jumps and sensor sweeps in order to find Atlantis.

McKay successfully completes modifications to a puddle jumper allowing it to open up a hyperspace window. They travel to the Asuran home planet and once there, Weir's reactivated connection the other replicators allows her to share their knowledge. The ship extends an anti-replicator field down through the city's core and Weir guides Sheppard and Ronon to the ZPM room where they successfully remove the module and return to the ship.

Once back at the jumper, McKay informs them they burned out the drive on their first jump and he'll need to tie the ZPM into the systems to boost the power. In the meantime, he's discovered that the Replicators' programmed command to attack the Wraith was shut down. He wants to reactivate it but Ronon and Sheppard must go deeper into the core with a computer pad to upload the data to the systems.

With Weir's guidance, they find the right location but the pad doesn't work. Adjustments need to be made and they are running out of time. The replicators are getting closer and closer to adapting to the field and are sacrificing themselves to do so. Weir takes matters into her own hands and goes down into the core where she runs into Oberoth and accesses his brain in the same way he once did hers. She creates a scenario in which he comes to believe he has captured all of the team, giving Sheppard enough time to adjust the computer and activate the command. They manage to escape but are forced, on her insistence, to leave Elizabeth behind.

Back in the jumper, McKay, Ronon, and Sheppard attempt to escape but the Replicators are on their tail and their weapons are down. With spectacular timing, the Apollo appears to help them, taking the brunt of the attack so they can make their way into the ship's bay.

Back on Atlantis, the ZPM is installed and the city makes the jump to hyperspace to a planet Weir knew nothing about and therefore the Replicators cannot take that information from her. John successfully set's the city down on the ocean. He later congratulates Carter on her promotion to Colonel. The city is now back in contact with Earth.

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Ronon rediscovers old friends, Ara, Tyre, and Rakai skilled Satedan fighters who urge him to join them permanently. He seriously considers their offer particularly when Colonel Carter, recently arrived to take charge of the city, turns down his request to have his friends visit the city. He agrees to undertake a mission with them to destroy a Wraith lab where Wraith scientists are working on a way of shutting down the replicator code that causes them to attack Wraith.

Though wary of Ronon's friends, Sheppard and the rest of the team agrees to hear out their plan after they inform them of the Wrath's intentions. Carter agrees to the mission and the team sets off to infiltrate the hive. The two teams separate and Sheppard and Teyla are taken prisoner. McKay momentarily escapes only to be stunned and turned over to the Wraith by Ronon's friends who are actually working for the Wraith.

Ronon escapes and returns to Atlantis where a rescue mission headed by Carter is launched. In the facility, the Wraith scientist demands that McKay undo the changes he made to the Replicator code, using a captured replicator as his way in. He stalls for time and when the rescue party arrives, the power to the facility is shut down freeing the replicator who begins attacking the Wraith. Ronon realizes that his former friends were broken by Wraith torture, and turned on two of their own who did not do the same. He fights and kills two of them before returning to the team.

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During an off-world mission Sheppard's team encounters a crystalline life form that throws Sheppard back after he touches it. The team returns home and all are assured by Dr. Keller that they are medically fine. Teyla experiences a horrifying nightmare involving Sheppard as a menacing force. Keller and Ronon also have nightmares involving Sheppard.

Though there is little evidence, the team contemplates that they may have brought back a malevolent entity with them, one capable of traveling from person to person after first having imprinted on Sheppard. They realize the entity may be able to travel by way of conductive material. After avoiding a near crisis involving a sleep walking Evan Lorne, the team determines the entity now rests within Dr. McKay.

They place McKay in a room without conductivity and try to solve the problem before McKay falls asleep. When Sheppard wonders if entering McKay's dream could lead to a solution, Carter recognizes a new use for technology acquired from a Milky Way race. Using virtual reality technology, Sheppard enters McKay's dreams to help him fight his fears, represented by a version of Sheppard.

When McKay crashes, the entity turns against Sheppard and the two begin to fight. On the verge of losing, he's given a second wind when McKay enters his dream to help him fight. Sheppard manages to overcome the alien and throw him through the stargate. Later, the team returns the entity to its home planet.

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On his way back to the space gate after visiting an Atlantis base on a primitive world, Sheppards' jumper is attacked and captured by a mysterious race of humans. Known as the Travelers, they live out their lives on board ships equipped with hyperdrives. Their ability to traverse space has kept them safe from the Wraith for thousands of years but now their numbers have grown too large and they have even been forced to abandon some of their own on planets.

The leader of the Travelers, Larrin, tests Sheppard's blood and determines that the possesses the Ancient gene and suits their goals. Having heard that a new powerful group of humans have been battling the Wraith using Ancient technology, the Travelers set up spy sattelites around various worlds to track and capture Sheppard. She intends to force him to initialize the functions of an abandoned Ancient vessel hoping they'll be able to reverse engineer the interface.

Once on board the Ancient vessel however, Sheppard uses the opportunity to send out a message via morse code and choses not to react the inertial dampeners before starting up the ship's engines, knocking his Traveler guards unconscious. Unfortunately, his communication attempt draws the Wraith and they are soon engaged in a battle. Sheppard manages to destroy the Wraith vessel but not before all the Travelers but Larrin are transported by the Wraith and several Wraith beam on board.

Working with Larrin he manages to take out two of the Wraith and forces the third to return the life force he has taken from Larrin and leave. Despite their new rapport, Larrin recaptures Sheppard at first opportunity. Sheppard informs her that had she simply asked for their help, things may have turned out better but she could not risk the chance they'd say no. He also informs her that her people would do better to form an alliance given their advanced technology as the Wraith are fighting a new enemey that could tip the balance in the favor of humans in the galaxy.

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After an expedition to the mainland to collect botanical samples returns to Atlantis, several individuals begin experiencing severe headaches which eventually lead to memory loss. Soon the whole city begins to fall ill except for Teyla and Ronon. Studies identify the culprit as a bacteria similar to one found in Athosians that causes an illness common in childhood throughout the galaxy. An herbal treatment is easily available and can be found on the mainland. However, by the time this conclusion is derived most of the city have lost their memories and become suspicious and afraid. Teyla attempts to help McKay hold it together in order to complete a program that will allow the distribution of the cure through the city's ventillation system, once Sheppard and Ronon return from the mainland with samples of the plant.

Hyped up on stimulants to delay the effects of the illness, Lorne and his men patrol the city rounding up civilians and grouping them in the mess hall. Not recognizing Teyla, they suspect she is the one responsible for their demise and lock her in a cell. With Teyla gone, McKay films a message for himself to remind him to find Teyla, the only one who can explain what has happened. He later loses memory of those events but the message and picture of Teyla cause him to seek her out. He is intercepted by Lorne and placed with the others but he manages to convince Carter to escape and help him search for her. They run into a confused Zelenka and together they manage to find Teyla who informs McKay that he needs to complete his program. Though he doesn't know how, Teyla encourages him to try. Fortunately he was almost done and simply pressing enter completes the task.

Sheppard becomes confused on the mainland forcing Ronon to tie him up while he searches for the necessary plants. Sheppard escapes but Ronon manages to convince him to trust him as it can't be worse than what he has already suffered. They return to Atlantis but are accosted by Lorne who thinks they may be an invading force. Ronon manages to convince him, using an image Sheppard gave to Lorne to remind him who he is.

The plant succeeds in curing the populace but recovery speed varies. McKay worries that Katie may not recover as, after a day, she still has not awoken. She eventually awakens and is as relieved to see him as he is to find she is OK.

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Dr. Jennifer Keller joins Teyla on a visit to New Athos where Keller plans to do routine examinations on the populace. They find the Athosian camp deserted and discover a violent and primitive tribe known as the Bola Kai are in the area. They are unable to make their way back to the gate as the Bola Kai are guarding the area. They are seen but manage to elude the Bolokai, however Keller twists her ankle. A hunt is on for the two women and Teyla kills three Bola Kai hunters in succession. Keller must overcome her fears and lack of survival instincts to keep up with Teyla and elude the men after them. Weapons stashed for the Athosians in time of trouble are missing but the Bolokai do not have them in their possession.

When Keller comes across a wounded man, Nabel, who appears Athosian but later claims to be Genii, she is determined to help him despite Teyla's warnings. The man claims he was sent to infiltrate the Athosian camp and that the Athosians were culled by the Wraith after being led to the planet by Wraith-worshiping Bola Kai. His injury and Keller's twisted ankle only slows them down however and the two are captured by the Bola Kai who demand to know where they are from. Teyla refuses to tell them anything but Keller gives them the address to an uninhabited planet to buy them more time. Keller believes the Bola Kai are as they claim, not Wraith worshipers and their leader also claims they only arrived after the Athosian camp was deserted.

Teyla and Keller are rescued by Nabel who has acquired a gun. He turns on them however, demanding the gate Address to Atlantis. Keller realizes he is not Genii and it is he who is the Wraith worshipper. Nabel implies that the Athosians may be still alive. Teyla and Nabel fight and she is taken down but Keller attacks and manages to grab his gun and shoots him in the thigh. Teyla demands to know what has happened to her people but before she can get answers, the Bola Kai attack. Fortunately, their rescue arrives.

Realizing that is unlike Teyla not to check in with Atlantis, Sheppard , Ronon and McKay visit the planet in a puddle jumper to check on the situation. They manage to get Teyla and Keller safely back to Atlantis. Teams later check on the planet but find no remaining life signs, not of Nabel, the Bola Kai or the Athosians.

Having faced the possibility of never seeing her father again, Keller plans to return to Earth to visit him. Teyla is determined to find her people and vows vengeance against whoever took them. Before she can return to duty however, Keller tells her they must discuss her condition.

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Desperate for news on the location of her people, Teyla convinces the team to go see a seer, Davos, whose ability to see the future may be of help. Their visit to Davos' home planet surprises them as they are greeted at the gate by Davos' daughter, aware of their intentions. Davos is extremely ill but able to share his prophetic visions with Rodney of a future capture of their team by the Wraith on a misty world.

The team returns to Atlantis and Keller visits Davos and determines he has cancer. While Davos is brought to Atlantis for tests and treatment, the team prepares to fulfill Davos' and Rodney's vision after hearing from another offworld team that a Wraith desires a meeting with John and have designated a meeting site (M2R-441) that matches the vision. The team prepares for the trap despite Woolsey's concern. Woolsey is visiting Atlantis on behalf of the IOA to evaluate Colonel Carter's leadership.

On the planet, Davos' vision is fulfilled exactly but the team is prepared and returns with a Wraith prisoner, the same Wraith who helped Sheppard escape the Genii ("Common Ground"). Their Wraith prisoner informs them that he needs to know what Rodney did to alter the Replicator base code. The virus the Wraith used years ago to shut down the Replicators desire to attack them, is no longer working.

Though the team is unsympathetic to Wraith problems, they change their mind when they learn that the Replicators have a new tactic. They are attacking human worlds, wiping out the Wraith food source, humans. This ties in with their previous use of a virus discovered on Atlantis ("Hot Zone"). A probe sent to another planet, confirms the complete destruction of the world inhabited by over 50,000.

Dr. Keller confirms that Davos has terminal cancer and she can do no more than handle his symptoms. Davos informs Carter that the galaxy is at a crossroads and its fate rests on what the expedition does. He shares with her a vision of the destruction of Atlantis and that of a hive ship above the city. He also confirms for Teyla that her people are alive, though he doesn't know where and like Keller tells her she'll have to tell the others about her pregnancy soon.

A Wraith vessel appears in orbit and their Wraith prisoner informs them that the vessel is his. The ship tracked an implant emitting a signal. Despite Woolsey's objection, the team is caught in a difficult situation and must make a decision. Carter is worried that whatever they do will lead to Atlantis' destruction as she saw in Davos' vision. Sheppard prepares to destroy the ship if they show hostile actions. Carter gives the go ahead for Rodney to work with their prisoner in trying to complete a new virus. Woolsey objects given their last alliance with the Wraith did not go well ("Allies").

After some work, Rodney discovers their Wraith has not given them the full virus and may be preparing to doublecross them. Their suspicions grow as a new hive ship makes its approach. They worry this may be the vessel that destroys them. If they shield the city, the Wraith will know Atlantis' location and if they try to destroy them they may send a message to other Wraith about the city's location. If they cloak the city and the new ship learns from their prisoner's vessel of what is going on, they are vulnerable without a shield as switching from one to the other is time consuming. Their prisoner encourages them to cloak the city and Carter agrees. Woolsey objects and tries to belay Carter's order to hold off on an attack against the ship to see their intentions. The new ship powers weapons but does not attack the city, instead the two destroy each other before sending any subspace messages.

Davos dies on Atlantis and is taken home by his daughter to be buried. Carter and Sheppard remain concerned about Atlantis' future destruction as none of Davos' visions have ever failed to come true. He appeared to have developed some of the Ancients' advanced brain functions but did not continue progressing toward ascension.

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When McKay and his team hit a wall in their work on a means of shutting down the replicators, Zelenka recommends he call on his sister, Jeannie, for help. Shortly after emailing her the problem, she is kidnapped from her home. McKay, Sheppard, and Ronon visit Earth to find out why and who is behind it.

McKay promises his brother-in-law, Kaleb that he will her her back and sets to work tracing who was keeping track of her emails. He quickly finds a trail and he and NID agent, Malcolm Barrett follow it without waiting for backup. Barrett is knocked unconscious and McKay is taken prisoner and soon finds himself in a computer room with his sister.

Their kidnapper is Henry Wallace, head of Devlin Medical Technologies (DMT), a government contractor who has been fed a steady stream of alien technology by the government to be adapted for regular use. DMT is also the maker of the subcutaneous transmitter McKay is equipped with which allows them to easily shut it down making McKay and Jeannie's rescue unlikely.

Wallace has kidnapped them in order to save his daughter who is dying of leukemia. Desperate for more time, he injected her with nanite prototypes hoping to heal her. instead, they are doing more damage, leaving her with only days or hours to live. McKay initially tries to escape but the two are recaptured and to ensure that they solve the problem, Wallace injects Jeannie with the same nanites. Though he knows he'll go to prison he's determined to save his daughter.

While Ronon, Barret, and Shepard pore over paperwork, hoping to find a clue to who has taken McKay and Jeannie, McKay and Jeannie work on solving the nanite problem. They come up with what they believe is a solution and it is immediately in Wallace's daughter, Madison. She begins to recover but two hours later, her heart stops and nothing can revive her. A few minutes later however, her heart restarts and she wakes up. McKay realizes that after fixing her leukemia, the nanites continued to work and needed to shut down her heart to fix it. However, her brain has been without oxygen too long and she is no longer the same girl. This has dramatic implications for Jeannie, as without an illness to fix, the nanites will attempt to fix epilepsy in her brain.

Focusing on The Trust as the responsible party has slowed down Sheppard's progress but once they put that idea aside they eventually pinpoint DMT. They find Sheppard and McKay and arrest Wallace. McKay and Jeannie are transported to the SGC via the Daedalus's transporters. She is put into a coma and her legs are broken to delay the nanites by giving them an injury to fix.

McKay attempts to come up with a solution but he's running out of time. Desperate, he asks for their Wraith prisoner to be transported to the base to help him. He begs him to help him not for his sister but for the potential gain in knowledge of how to shut down the replicators. The Wraith agrees but he becomes weak and is unable to finish without feeding. McKay informs Sheppard that he is going to volunteer to be fed on. Jeannie is running out of time. He has learned that Madison has died when an artery ruptured when the nanites ran out of power in the middle of the task. The same is likely to happen to Jeannie.

McKay is determined he must sacrifice himself for his sister particularly as the whole situation is his fault. Sheppard refuses him however and locks him out of the lab. Sheppard visits Wallace in jail and shows him pictures of Jeannie and her husband and daughter and tells him how his actions will result in the loss of a mother and wife.

Later, McKay returns to his lab and attempts to gain access with no success. The door opens and reveals Sheppard and a now energetic Wraith as well as a dead body being wheeled out. The body is that of Wallace whom Sheppard claims volunteered to be fed on to right his wrong. The Wraith completes his work and Jeannie is saved and returned to health.

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McKay performs a gate diagnostic that renders the gate inoperable but a greater problem arises when a chunk of metal that appears to have been sot down falls into the city. On examination, McKay recognizes what he believes to be replicator code but Zelenka counters that it may have been something else. Before they can examine it further, it shuts down the computer and later explodes, destroying McKay's lab.

While sparring with Ronon, Sheppard sustains an injury that requires stitches but a visit to the infirmary reveals no injuries. He requests a full body scan and blood test but Keller finds nothing. Ronon believes people in the city are behaving oddly. The team gathers to discover what might be going on and search a record of the infirmary tests on Sheppard but find nothing. They conspire to return to the infirmary when it is empty but a city scan reveals no other inhabitants but themselves.

In the infirmary, Sheppard and Teyla perform a test that reveals his body is teeming with nanites. The team regroups and discovers they all are able to heal immediately after injury. Keller arrives and reveals that they are not on Atlantis and she is actually a replicator, as is everyone else in the city but for them. They, as well as Dr. Weir whom they discover, were all recreated biologically with the aid of nanites as a part of the replicators' desire to achieve ascension.

Their experiments were not sanctioned by Oberoth and the others of their kind and is a direct result of Dr. Weir's influence. The probe they discovered was sent by other replicators who soon arrive and begin attacking the city. Weir manages to convince the Keller replicant to let them go so their work won't be in vain. Keller gives her a data module that will allow them to find all Aurora class replicator vessels in the galaxy.

The team escapes the city's destruction via puddle jumper and attach themselves to the attacking replicator vessel. They plot to steal a ship once on the replicator homeworld. They succeed in doing so and once able to, contact an offworld Atlantis team and make contact with their Atlantis counterparts.

Both teams meet and the two Rodney's immediately bond. Both McKay and Sheppard are happy to see Weir again, though she points out that she is not actually the original, who is truly gone. They are not long together before the replicators find them and attack. Determined to help where they can, the secondaries provide a distraction with the puddle jumper allowing the team to escape with the data module. Their jumper is shot down and they are found by replicator search teams.

On Atlantis, McKay works overtime trying to put the data module to use. He is devastated at having lost Weir and reflects on the loss of Carson as well. Though Zelenka attempts to help McKay buries himself in work to compensate. Sheppard finally realizes the Weir they lost will never come back and finally begins to pack up her personal belongings.

McKay's work bears fruit and Replicator vessels begin appearing on the computer. Though only a few initially appear, the Keller replicant seemed to have failed to convey the true scale of the replicators surge in ship building. More and more vessels continue to pop up on screen, seeming to match or even outnumber the known Wraith vessels in the galaxy.

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With information on the location of all thirty-seven Aurora-class Replicator vessels in the galaxy, the expedition begins planning for a means to stop the Replicators from destroying more human worlds. They've also begun evacuating planets in the path of the Replicators. The Daedalus and the Apollo and their captains, Col. Caldwell and Col. Ellis have arrived at Atlantis to provide support and have upgraded their weapons with plasma beam technology.

Though impressed by his own progress, McKay and his Wraith partner have not found a way to shut down the replicators. Ellis is angered by what he sees as McKay's wasting of their time but Colonel Carter chastises him for his rudeness and threatens to revoke her hospitality. The Colonel's fallback plan is to destroy each replicator ship with their weapons but McKay argues that merely leaves Replicator cells inert not destroyed. His method, should it work, would wipe them out completely. He requests more time to work on it. Carter gives him ten hours.

Hours later, McKay is still stalled and plan B is put into action. The Daedalus and Apollo manage to destroy a Replicator vessels easily. A week later, several more vessels are destroyed and the Replicators fall back to their homeworld to formulate a new strategy and build more ships. Ellis sees potential to wipe them all out at once but the task is too great for only two ships. The team has approximately a week to come up with a new strategy of their own before the Replicators separate and head back out into the galaxy.

McKay still has no luck with shutting down the nanites. After contemplating using the Ancient anti-replicator technology to which the Replicators are likely immune, McKay hits upon a new solution. Rather than severing the connection between individual nanite cells, he wants to increase their attraction significantly. All nanite cells would be drawn together to the replicator homeworld, forming a superdense blob. Sheppard questions the possibility of creating one super replicator but McKay insists the nanite cells would need more time to adjust to their situation before they fuse too tightly together and become inert. Carter believes his idea may have potential.

To complete the task, McKay plans to use the same machine the Ancients used to develop the Replicators. He wants to create a block of nanite cells that will spark the attraction to the other replicators. His initial attempts fail, however, as the machine was not designed to make blocks of nanites, but human form replicators. The idea is to visit the replicator homeworld, beam the blocks into a populated area and activate its programming. McKay then realizes that though the Replicators on the planet will immediately be affected, those in orbit will have time to escape unless they can formulate a distraction.

They face a problem providing such a distraction as they are hopelessly outnumbered. Sheppard has an idea to get more ships however. They ask their Wraith prisoner for his help getting the cooperation of the Wraith and he agrees. Their Wraith must personally negotiate with others. Sheppard and his team visit the Wraith vessel where they are all stunned by the Wraith. When they awaken the deal is complete and they have gained the cooperation of seven Hives. It is not the twelve they were hoping for but without Queens some vessels fear they won't be able to replenish their numbers.

On their way back to Atlantis, the team runs into an Aurora-class vessel captained by Larrin. She intended to investigate the meeting of several Wraith vessels. The team manages to negotiate for her people's help in their plan. On their return to Atlantis, Teyla decides to check in with the infirmary, surprising both Sheppard and Ronon. She reveals she is three months pregnant and has known for almost two months. Sheppard is extremely angry with her for the risk she's taken and removes her from active duty immediately. Ronon however, is more supportive realizing the child's father is among the missing Athosians and assures her they'll find him together.


After several failures getting the nanite blocks to maintain cohesion, McKay decides to create a human form replicator, which was the real purpose of the machine. He names his creation FRAn (Friendly Replicator Android). FRAn has all the intelligence of her brethren but is willing to go along with McKay's plan. She finds that his calculations may be slightly off. She estimates the nanite cells will adapt faster to their circumstances than he believed. The mass will be able to manipulate itself before reaching critical mass and stop the process. She has a solution however, overloading the ZPMS around the mass causing them to be further compressed and ultimately destroying the planet. To do that, McKay, Ronon and a team of marines will need to beam down to the planet to overload the ZPMs. Sheppard will operate the chair on Larrin's ship.


The plan goes into action and the Travelers, Daedalus, Apollo and several hive ships head for the Replicator homeworld. FRAn reveals that she's excited about their plans and not at all concerned about her soon to be nonexistence. She wishes him luck on his mission. Both are beamed down to the replicator homeworld to begin their respective missions. In orbit, the battle ensues and several Wraith, and Traveler vessels are destroyed.

McKay completes his action and FRAn activates. The replicators are drawn to her, on the planet and from space. The nanites form an enormous mass on the planet. McKay is unable to set the ZPMs to overload as the mass has interrupted power systems causing a blackout. They are running out of options but Carter realizes that the city rests on a vast deposit of naturally dense neutronium. McKay can increase the attraction between the cells so they attract the neutronium increasing the density and causing the mass to sink to the planet's core where the pressure will increase significantly, resulting in an implosion that will destroy the replicators and the planet. The plan succeeds and the fleet leaves the system.

McKay deletes the Replicator homeworld M7R-227 from the database.

Back in the Replicator system, a ship is seen in the system checking for trace replicator cells. None are detected. A woman in black who appears to be Elizabeth Weir states that they can finally get to work without looking over their shoulders.

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Atlantis picks up a signal from their former Wraith associates' transceiver and Sheppard's team plans to investigate. Though Teyla wants to join the mission, Sheppard turns her down, insisting she get used to the idea that she won't be able to do all she used to, not even to find the father of her unborn child and the other Athosians.

When the team investigates the signal, they discover an abandoned and damaged Wraith vessel and learn from the logs that the ship was headed to a planet the Wraith consider extremely important. Sheppard returns to Atlantis to gain Teyla's help in flying the Wraith ship and makes a compromise. He would decide what missions she goes on.

When they return, Teyla whose mental abilities appear enhanced, flies the hive ship to a planet where another Wraith vessel, likely the same one that inflicted the damage on the vessel they acquired, is in orbit. They settle around a moon outside the ship's sensor range and take the jumper down to the planet, leaving Lorne and Teyla on board the wraith ship.

On the planet, they discover a vast Wraith facility where a queen appears to be sleeping in a chair. They realize that it is a breeding facility, with thousands of pods. They find their former Wraith associate is in prison and the queen, awakened by her minions, has called for him so she can feed on him. They manage to rescue him and he informs them that this is actually a cloning facility. After retrieving a ZPM from the Replicators' homeworld, he was able to restart production but was betrayed by one of his fellows who took the necessary power source to another hive. The ability to quickly clone soldiers, after stealing ZPMs from the Ancients was how the Wraith grew quickly in number and defeated them in the war 10,000 years ago.

Sheppard and his team are captured but their Wraith associate escapes. They are brought before the queen who tries to gain information from Sheppard, and threatens to feed on Rodney. She suddenly changes her mind, however, and sends them back to their cells.

On board the Wraith vessel Teyla and Lorne are contacted by an approaching drone. It belongs to the Wraith they worked with previously. He informs them of the situation and wants to abandon the rest of the team and return later. Teyla refuses and finds an alternative. She makes contact with the mind of the Queen on the planet and manages to prevent her from killing the team and ultimately forces her to free them from their cells. However, the Queen also has access to Teyla's mind and tries to find a way to kill the mind of the child inside her. Sheppard kills the Queen in time to prevent that and they manage to escape.

With pods in the facility lighting up, they are unable to overload the ZPM and must abandon the facility. In orbit, the other Wraith vessel has discovered the Wraith vessel Teyla and Lorne are controlling and open fire. The rest of the team manages to make it back to the ship and Sheppard asks Teyla to set the ship on a collision course with the Wraith facility. With the facility destroyed, the team returns to Atlantis. Their Wraith escaped to unknown parts.

Teyla admits to John that he was right about the risk of bringing her on missions. The prospect of losing her baby proved sobering. Only John's quick actions prevented her son from dying.

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McKay informs Sheppard that he plans to ask Katie to marry him. Shortly after entering her garden workspace the city goes into lockdown, presumably having detected a virus. With communications down and no access to his computer, McKay begins to panic and comes to believe he has been infected and he and Katie are both going to die.

Ronon becomes locked in the infirmary with Dr. Keller. The two try to devise an escape but their Jaws inspired oxygen tank bomb fails and Ronon is forced to admit the doors are stronger than a shark. Ronon reveals that he wasn't sure Keller would fit in when she arrived, believing at the time she was weak. She reminds him of the woman he loved on Sateda. Keller reveals that she has never fit in anywhere, having missed out on many social events after graduating high school at fifteen and being far too young for college social events.

Carter and Zelenka are trapped inside a transportation booth and Carter tries to access the mainframe to discover what is really happening. She is unable to make any changes but learns that the city may be reacting to a shift in the planet's ionosphere rather than an actual outbreak. A mistake on Zelenka's behalf fries the computer shortly after.

Teyla and Sheppard are trapped together and he worries that, as often happens in movies, she'll go into labor. Teyla experiences some discomfort and Sheppard decides to climb four stories up the outside of the building to the control room where he hopes to end the lockdown with the aid of Rodney's password which he memorized. He succeeds in getting there and enters the code which starts the self destruct countdown and shut down all computer systems completely.

They must find away to shutdown the self destruct at its source. Sheppard, Lorne and two others climb back down the building and once back inside manage to free Zelenka and Carter from the transporter. Unable to use the doors, Zelenka volunteers to enter a ventilation shaft that leads to the self destruct system's power center. Zelenka manages to shut down the system and end the lock down.

McKay's panic leads him to realize that his gloom and doom outlook is an indication that he may not be ready for marriage. Katie agrees and tells him goodbye, signifying the end of their relationship.

Ronon and Keller bond and almost kiss before the lockdown goes into effect, freeing them.

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McKay and Sheppard visit a regular trading partner and are asked to escort young princess, Harmony, the youngest of the recently deceased queen and her chosen successor, on a journey to the temple of Laros in the forest. On the way they encounter Genii soldiers who try to kill them and their charge.

One of Harmony's sister has arranged for her to be killed so she can become queen and renew their trading partnership with the Genii. Though Harmony, a bratty thirteen-year-old conflicts with McKay and immediately falls in love with John, she eventually switches her affections when it is McKay who saves her life when Genii soldiers attack them at the temple's ruins.

Sheppard is able to ward off the soldiers using the ancient mini drones housed in the Ancient ruins. Harmony is destined to control the drones as proof of her right to be queen but can only activate it to prove her leadership after McKay fixes the device and Sheppard uses it against the Genii. Harmony accuses Sheppard of usurping her role in activating the device to stop their attackers. The two successfully return Harmony home where her sister is imprisoned for her crime and Harmony takes the throne. She memorializes McKay's heroic efforts in a painting that decidedly discounts Sheppard's efforts.

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On leave on Earth, Sheppard learns that a human-form Replicator engineered by scientists is loose on the planet.

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McKay, Carter, and Keller become trapped in an underground chamber while on an off world mission.

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Teal'c visits Atlantis to counsel Ronon on his upcoming IOA review.

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A mysterious illness spreads across the galaxy. Teyla is convinced her child's father is trying to communicate with her.

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An old friend returns shocking the team. Teyla tries to escape captivity.

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Sheppard returns to Atlantis to find it abandoned and in the midst of a desert.

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