A man wakes up in the Atlantis infirmary, restrained and surrounded by medical equipment. Upon seeing this, Dr. Beckett summons Dr. Weir. The man is told that he is recovering but from what he does not know; he appears to have lost his memory. He is re-introduced to Weir and Sheppard. Weir tells him that his name is Lt. Michael Kenmore and that he is in Atlantis. Sheppard tells him that he was part of an off-world team and was captured by the Wraith. He finds the Wraith to be somewhat familiar. Dr. Beckett tells him that he has been unconscious for days but that he is now doing well.
Weir, Beckett, and Sheppard observe Michael from the gallery and Weir tells them to keep an eye on Michael because they must proceed with caution and trouble may be ahead.
Dr. Beckett gives Michael an injection for his Diabetes. He tells Michael that he appears to have amnesia from trauma, probably caused by the Wraith. Teyla enters the infirmary and asks to speak with Michael. She notices that Dr. Beckett appears exceptionally tired and tells him to get some rest.
Teyla then goes to Michael's room and he recognizes her. He asks if they were friends and she says they were. She tells him a little about himself, that he is a great soldier, and that he sacrificed himself to save his team. He responds that she is even more heroic since she helped to save him from the Wraith.
Dr. Weir, Teyla, Sheppard, Beckett, and Dr. Heightmeyer discuss Michael's progress. Beckett and Dr. Heightmeyer think that he would do well to be around familiar surroundings but Sheppard is apprehensive. Dr. Weir decides to release Michael from the infirmary.
Teyla escorts Michael to his room and shows him around. She tells him that he is from Texas—he even has a cowboy hat. He sees a photo of his parents but does not remember anything yet. All the while he is being monitored.
Later in the commissary, Rodney is upset that his favorite blue Jell-O is no longer on the menu. He goes over to Michael who is eating while being watched by two bodyguards and introduces himself. After exchanging platitudes Michael recognizes the tablet Rodney is holding has displaying Wraith materializer schematics. McKay tells him that getting those schematics was part of the mission in which Michael was captured.
Michael spars with Teyla but is not doing well. She tells him that he is in fact a very good fighter and they continue to spar. This time Michael does better and pins her but is suddenly attacked by Ronon. Teyla tells Ronon that she is fine and tells him to release Michael.
Dr. Heightmeyer talks with Michael in therapy. She tells him that Ronon is still new and adapting to their ways. They discuss his memory loss; he wants to get back to normal and she affirms that he needs to give it some time.
Michael awakens in a cold sweat from a dream of being on a Wraith ship. He gets a glass of water and when he looks in the mirror instead of his own reflection, he sees a Wraith hissing back at him. He jumps up again. Michael talks with Teyla and tells her about his dream. She explains that it is due to all the stress induced by the Wraith and that she gets them too.
Dr. Weir asks Teyla about the dream and Dr. Beckett if he can do anything to help Michael. Beckett recommends against increasing his medication. Teyla wants to tell Michael the "truth" because she is having difficulty keeping it from Michael and does not believe withholding it is the correct action.
Michael wakes up startled again.
Dr. Heightmeyer has another session with Michael and he tells her that he thinks everyone is keeping a secret from him. He thinks that the Wraith did something to him but nobody will tell him what.
Sheppard and Ronon bump into Lt. Kenmore the next day. Dr. Beckett has given Michael some more medication and he is going to try to get some sleep. Michael tries to apologize to Ronon for whatever it is he did to make Ronon upset but Ronon will have none of it. He tries to tell Ronon that he just wants to bury the hatchet but Ronon punches him. Michael returns the blow and Sheppard and the "bodyguards" break up the fight.
That night, Michael is not able to sleep so he goes—escorted by the two guards—to see Dr. Beckett. He gets to the infirmary but Dr. Beckett is asleep. He notices a calendar on the wall from the Kenmore Company. He tries to access the computer but is prompted for a password. Michael finds a case with some medical discs containing files and video about him and sneaks them out.
Back in his room, Michael takes up his computer and turns to avoid a surveillance camera. He inserts the last disc and sees footage of himself from just before he woke up. He checks the next disc and sees himself struggling in pain. An earlier disc shows him demanding in a deeper voice to be released. An older disc still has him being held down by Ronon and Sheppard has he screams in a deep voice that they will die. The footage cuts to a frontal shot and we see a WRAITH! Dr. Beckett enters Michael's room accompanied by security. Michael questioningly, and with a scared and confused look, turns the computer to display to Dr. Beckett the frozen image of himself as a Wrath.
Michael is furious. He confronts Weir and accuses her of lying to him and demands an explanation. She tells him that the Wraith evolved from the Iratus bug which became more like humans which it fed on. Dr. Becket tells him about the retro virus he created to suppress the Iratus bug DNA, leaving only the human DNA, effectively transforming a Wraith into a human. Once they had a viable drug, they decided to test it and Michael was their subject. Michael asks about his "insulin". Beckett explains that once the transformation is started, another drug is required to keep the Wraith element from returning. Michael feels like they think being a Wraith is a disease and that they can cure it. He asks what right they have to do this to him and Sheppard justifies it by saying that they are defending against the Wraith. Weir says that it was her decision to keep the truth from him and to create the false history; that if he knew the truth he might react like he is now. Sheppard says that the point of the experiment was to eliminate all traces of Wraith from him and that he is better off as he is now.
At a meeting, Ronon thinks the experiment is a bad idea but Sheppard disagrees because the drug is working. He proposes that they hit entire hive ships with it to turn them into humans. Beckett warns that the virus is not ready for that yet and that he does not yet know the dose required to make the change permanent. Ronon insists that despite changing how they walk, talk, or look, nothing they do will ever change the Wraith into real humans; they are still, and always will be Wraith.
Teyla visits Michael in his room. She had told him that she rescued him when he was captured by the Wraith but he now understands who did the actual capturing. He is insulted that she said she is his friend. She says that she wants to be and that being human will make his life better. He counters that they did it to make their own lives better. He then asks what makes the Wraith so bad. Teyla gives some examples including the fact that the Wraith have no compassion but Michael challenges her with their own actions; what they did to him was no more compassionate.
Michael has a session with Dr. Heightmeyer who tries to discuss his feelings of betrayal which he ignores. He tells her that he is beginning to understand the strange feelings he's been having. He realizes that they are basic Wraith instincts like hunger and aggression that he can't shake and that now that he knows the truth he feels them even more.
Dr. Weir is concerned about Michael's Wraith compulsions and asks Beckett if he can suppress them. Dr. Beckett says that he could try increasing the dosage—assuming of course that Michael agrees to take it. Sheppard says that if he doesn't agree they will have to force it and that maybe another big dose will wipe his memory again. Teyla asks what they would do then; lie to him all over again?
Michael is summoned for his injections. He goes along, escorted by the two guards and Ronon. He confronts Ronon who tells him that he is waiting for Michael to give him a reason to kill him. Michael thanks Ronon for being the only one honest with. They continue to the infirmary but Michael attacks the guards, steals a weapon, and runs off. Ronon pursues Michael.
A guard happens upon Michael who then shoots him. Having killed someone, Michael gets a strange sensation. Ronon approaches Michael and is about to kill him when Sheppard runs in and stuns Michael.
Dr. Weir tells the others that they cannot keep Michael on Atlantis anymore because it is too dangerous. Sheppard suggests taking him to the Alpha site after sedating him. Ronon asks what happens then. Dr. Weir says that the experiment would continue in an attempt to eliminate any remaining traces of the Wraith from him. Ronon does not like the plan—especially since Michael killed someone—and suggests killing him now. Dr. Heightmeyer denies the idea; they cannot just kill him. Sheppard says that if Michael was still a Wraith they would have killed him but Teyla says that they made him human and must treat him as such now, that he is their responsibility. Ronon argues again that Michael is not a human, he is a Wraith. Weir asks Beckett if it's worth continuing the treatments. Feeling unsettled by the whole experience but not wanting to have done it all for nothing, Dr. Beckett decides that they might as well try an increased dosage. Dr. Weir agrees that they can not just quit after all this and authorizes the move. Ronon is not pleased.
Michael is now being held in the brig. Teyla arrives to tell him that he will be transported to the Alpha site. Michael understands; they want to avoid having him learn more about Atlantis and possibly communicate that information to any Wraith ships that might come close enough. He explains that he did not want to kill Sgt. Cole, he just wanted to escape. She tells him that the experiment will continue, to fully transform him into a human, and that the alternative is death.
Dr. Beckett prepares for moving to the Alpha site by having the equipment he needs gathered. He tells Dr. Weir his feelings of guilt about this whole matter but she tells him it's all her decision, that she authorized it, and so she is responsible.
They are ready to transport Michael to the Alpha site so Sheppard goes to the brig and stuns Michael who is then sedated and placed on a gurney. Michael wakes up at the Alpha site strapped to a bed. Teyla gets up and goes to get him some food. Dr. Beckett works on refining the drug. Teyla returns with some rations and gives Michael a little but he does not want anymore. He tells her that she is different and that she is the only one that has been nice to him. While he talks he enters her mind and puts her in a trance. She frees him from his restraints. He gets up and thanks her then puts her in a headlock from behind.
Beckett alerts Sheppard and Ronon to the situation. He tells them that Michael has taken Teyla hostage and has headed up the ridge. Somewhere in the forest, Michael ties Teyla's hands and tells her that he will not be experimented on anymore. He then forces her to march.
Sheppard follows Ronon as he tries to track Michael but Ronon has some difficulty since Michael has left no trail. Michael dials in an address on the DHD to activate the Stargate. Teyla secretly scrawls the address on a rock behind her. Sheppard and Ronon arrive at the gate just as Michael jumps through it, taking Teyla with him.
Michael and Teyla arrive on another world at dusk. Sheppard is about to summon McKay to extract the address that Michael dialed but Ronon sees the stone that Teyla marked.
While walking through the woods Teyla senses Wraith nearby. She turns around to see Michael reverting to his original form.
Closer to nightfall, Teyla wakes up with her bonds cut. She sees a Wraith ship unloading numerous Wraith soldiers. Michael says that this is what he was drawn to. She warns that the Wraith sense them and that they are coming. Michael is aware of this and intends to return to them. She says that they will once again be enemies but he says they never stopped. She asks if he will feed on her. He does not want to but is finding it difficult to resist. She tells him to go ahead. He tries to but pulls back. Suddenly he reaches out to feed on her but is shot by Sheppard and Ronon. Wraith soldiers approach and begin shooting so Sheppard, Ronon, and Teyla retreat. The Wraith gather around Michael and find him alive.
Later on Atlantis, Sheppard reports that Michael is almost completely a Wraith again. Beckett says that he is reverting faster than they had anticipated. Ronon says that he should have killed Michael when he had the chance and Rodney agrees because not only is Michael back with the Wraith but also knows that Atlantis still exists. They expect another wave of hive ships to be on the way, and this time, cloaking Atlantis will not likely work. Weir says they need a new defense plan and Sheppard says they need more firepower.