Ronon, Sheppard, and McKay watch as Dr. Keller examines Carson Beckett to determine if he's really who he appears to be. Keller confirms it is actually Dr. Beckett. Afterward, McKay goes to talk to his friend and Beckett explains he's been captive for two years after they met with Michael and his men. Michael took him along and forced him to help with his experiments by killing hostages. Mckay informs him that they weren't aware he was missing, and they rescued a Dr. Beckett. McKay also informs a shocked Beckett that Weir died.
Michael and his human-Wraith hybrids take Teyla to a dead world where he's performing his experiments, and leaves her with the remainder of her people who haven't been converted.
Keller has confirmed that their Beckett's cellular aging doesn't match, indicating that he's a clone. They give Beckett the news and he's forced to admit they have no reason to trust him. Sam shares his concerns but Beckett gives them a planet to investigate and Sheppard takes a team. They end up in a bar where the bartender refuses to tell them anything and an ambusher attacks them from the shadow. Ronon takes him out and it turns out to be Nabel Golen, the spy who helped Teyla and Keller previously on New Athos, and also tried to kill them. Beckett and Keller work together to save Nabel, but Beckett collapses to the floor. He's suffering from necrosis as his cells aren't reproducing fast enough to maintain his body functions. They quickly figure out Michael was giving Beckett a drug to keep him alive, but they can use the scans they took when he was brought back to come up with a cure. Beckett insists on helping to find the cure.
The imprisoned Teyla tries to get through to Kanaan but he simply walks away. Later, the hybrids come to get Teyla, knocking aside the Athosians.
Beckett and Keller run into a dead end as Beckett's condition worsens, and he refuses to go into a stasis pod.
Teyla is brought into Michael's lab, which contains Athosians in various states of transformation. Kanaan guards her and she tries to get through to him. This time he starts to recognize her but reverts to his normal zombie-state when Michael comes in and prepares to examine her.
Sheppard and others interrogate Nabel and suggest he provide them with help in returning for transporting him out of the Pegasus Galaxy.
Michael begins to scan Teyla and determines her child is healthy. He explains that since Teyla and Kanaan both have the gift, their child may have similar or even greater powers. He gives her an injection and says he can't afford to let anything happen to the child.
Nabel gives up the address of Michael's base and Beckett provides information from when he was once there. He insists on going on the mission and Sheppard and Ronon agree, but Rodney is angry they're willing to sacrifice his friend, and concerned that Beckett's condition is getting worse.
The team arrives at the base and Michael detects them, then destroys the hybrids undergoing transformation. He takes Teyla and heads for his ship, while his hybrids open fire. The team finds the Athosians and evacuates them then go after Teyla. The hybrids pin them down and Beckett runs off when they detect a ship preparing to leave. Beckett kills Teyla's guards but she refuses to leave without Kataan. Michael confronts them and Beckett pulls a gun on him, but is unable to fire: Michael has mentally programmed him to be obedient. Michael kills Beckett and leaves with Teyla.
Back at Michael's laboratory, Sheppard and Ronan combine fire on gas containers, and use the explosion to take out the hybrids. They go after Beckett and find him dying, and see Michael depart with Teyla.
Back at Atlantis, Keller warns that Beckett's body is shutting down and they have no choice but to put him in stasis. Rodney is trying to assure Beckett it wasn't his fault. They take him to stasis where Beckett asks Sam to deliver a letter to his mother, tells Sheppard to bring Teyla back, and gives Ronon a hug. Finally he thanks Rodney for his support and tells them all that it was worth it seeing them the last few days. Rodney promises to program some dreams into the stasis pod and then freezes him.