Ronon, Rodney, and Sheppard take Carson Beckett back to Atlantis where Dr. Keller examines him and confirms that he’s who he appears to be, rather than a Replicator or imposter. Beckett is sent to his quarters where Rodney comes in and discovers that Beckett believes Michael has held him captive for two years. The Atlantis team believed they had rescued Beckett, who later died in an explosion. Michael forced Beckett to help him with his hybrid-breeding program, and the doctor is surprised to hear that Atlantis didn’t even look for him since they believed he had died. He’s even more surprised to hear that Dr. Weir has died during his captivity.
Michael and his squad of Human-Wraith hybrids escort Teyla to an abandoned planet that Michael is using for his research program. Teyla is put in a large holding facility with the remaining Athosians that disappeared, including their leader Pauling.
Conducting further tests, Keller determines that the Beckett they have is actually a clone. He wants to help but has to admit that he could be a ticking time bomb planted on them by Michael. However, he gives them the coordinates of one planet he remembers from his time with Michael, and accompanies Sheppard’s team there. They go to a bar and try to get information on Michael from the bartender, but the latter refuses. Someone opens fire on them from the shadows, using a stolen Atlantis weapon. Ronon brings the man down and they take him to Atlantis. There Keller recognizes him as Nabel Golen, a spy working for Michael who interfered with her and Teyla on New Athos. Beckett helps her work on Nabel but collapse, and Keller determines that advanced cellular necrosis is spreading throughout his body. Beckett remembers being given regular injections by Michael, including one just before he was brought back to Atlantis. By comparing the scans taken from him then when he had the antidote, and now when he doesn’t, they hope to find a cure for his condition, or at least delay his death.
In the holding facility, Teyla tries to convince the converted Kanaan to release them, but he’s been too thoroughly brainwashed by Michael. The other hybrids take her away to Michael’s lab. It’s filled with tanks holding Athosians who he is preparing as hybrids, and Kanaan stands guard. She tries to get through to him again and he starts to overthrow his conditioning and free her. However, when Michael arrives Kanaan reverts back to his brainwashing and leaves her, while Michael prepares to examine her.
Sheppard demands Michael’s location from Nabel and they finally convince him to help by sending him back to Earth’s galaxy so he can avoid Michael’s far-reaching intelligence organization.
Michael scans Teyla and expresses concern for her child. However, it soon becomes clear that he wants to use the child, the offspring of two Athosians with mental powers, to develop even greater powers and implant them in his hybrids. He gives her a drug while saying he plans to make sure nothing happens to the child.
Having located Michael’s base from Nabel’s description, Sheppard has Beckett give them information on the interior layout. Beckett insists on going but Rodney is angry, believing they’re willing to sacrifice his friend because he’s “just” a clone. However, Beckett insists and goes on the mission. They arrive at the base but Michael detects them and prepares to evacuate while the hybrids hold off the Atlantis team. Sheppard and his men find Pauling and other Athosians and get them to the Stargate, then go after Teyla. The hybrids pin them down but Beckett runs on ahead when they spot Michael’s ship preparing to leave. He kills Teyla’s hybrid guards and tries to get her to come back, but she insists on finding Kanaan. Michael interrupts them and Beckett discovers he can’t shoot the human-Wraith: Michael brainwashed him into obedience. Beckett is frozen and Michael easily guns him down and leaves with Teyla.
Sheppard and Ronon break the deadlock by shooting compressed gas cylinders near the hybrid warriors, then go after Beckett with Rodney in tow. They find the injured Beckett and can only look on helplessly as Michael departs in his ship.
They take Beckett back to Atlantis and Keller has no choice but to put him in stasis. Beckett isn’t happy at being in stasis for an unknown period of time but has to agree. He says a farewell to all of them and enters the stasis pod, where he’s frozen.
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