Teyla is missing, a prisoner of the human-Wraith hybrid Michael. During a fruitless search for her, Sheppard's team discovers Dr. Carson Beckett imprisoned in one of Michael's bases. Of course, since Beckett died in an explosion in Atlantis over a year earlier, the team is more than a little disconcerted by this man who looks and acts just like him.
Back in Atlantis, as Dr. Keller tries to confirm his identity, Beckett tells McKay that Michael has forced him to assist with genetic experiments ever since capturing him two years ago on M8G-352, the planet where the Atlantis team marooned a group of humanized Wraith. McKay, confused, counters that his team rescued Beckett from that planet six months before the doctor died.
Keller's medical investigation explains this discrepancy: this Beckett is a clone of the original, created by Michael after the incident on M8G-352. Beckett is sobered to learn that the life he has been longing to return to throughout his imprisonment was never really his at all.
His personal distress aside, however, Beckett is eager to use his knowledge of Michael's operations to help rescue Teyla. The team knows that they could be asking for trouble by trusting a man who was created by their enemy, but Beckett's good intentions shine through and they decide to take the risk. On the first planet he leads them to, a stranger starts a gunfight with them. When they drag the injured man back to Atlantis as their prisoner, Keller recognizes her newest patient. He is Nabel Golan, the man who once tried to kill her and Teyla on New Athos. He works for Michael. After the team offers to protect Nabel from his vengeful boss, he tells them where Michael is holding Teyla.
Beckett recalls the location and wants to guide Sheppard's team again, but he has grown disturbingly weak. While he was a prisoner, Michael gave him injections of a mysterious drug that must have prevented his cloned organs from degenerating. Without it, his body is breaking down - he's dying. Keller urges him to enter an Ancient stasis pod while she searches for a cure, but Beckett insists on rescuing Teyla first. He accompanies Sheppard, McKay and Ronon as they infiltrate Michael's base.
Deep within that base, Teyla waits for rescue. While a prisoner, she has met a group of her fellow Athosians whose many failed escape attempts have left them in despair. She has begged Kanaan to help her, but though she has glimpsed signs of his old personality, he has been unable to shake off Michael's mind-control. She has endured Michael's eerie fascination with her unborn child. Now, as she hears distant shooting begin, she must hope that her friends can save her before Michael escapes with her to yet another of his hidden bases. Unfortunately, although Beckett's brave and compassionate heart has helped get the team this far, his mind - like Kanaan's - may prove unable to withstand Michael's psychic domination.