Lt. Michael Kenmore awakens in Atlantis's infirmary with no memory of how he got there - or who he is. Dr. Weir, Col. Sheppard and Dr. Beckett explain that he's a member of the expedition's military contingent who was captured by the Wraith during a dangerous mission. Although Sheppard's team rescued him, he was badly injured and has been unconscious for days.
Michael explores Atlantis, but even his personal quarters awaken no memories of his prior life. Instead, he notices that he can read and understand a Wraith schematic that Dr. McKay is studying. As if that's not unsettling enough, McKay's nervousness, Teyla's kind but evasive friendliness, and Ronon's obviously heartfelt desire to break his neck all force Michael to believe that there's much more to his story than anyone's letting on. Unnerved, he visits Dr. Heightmeyer, Atlantis's psychiatrist, who assures him that everything will be fine. But that night, Michael has a nightmare. He dreams he's a Wraith.
Teyla struggles to reassure him, but Michael becomes convinced that the Wraith manipulated his mind while he was their prisoner. Certain that the Atlantis team knows more than they're saying, he secretly searches Beckett's files and uncovers recordings from security cameras showing his treatment. There, he finally discovers his real identity: Though he's a man now, on the day he arrived, he was a Wraith.
His new knowledge forces the others to drop their act and tell him the truth. Michael was a Wraith warrior until Sheppard's team captured him and Dr. Beckett gave him an experimental drug therapy designed to turn Wraith into humans. Michael's anger at this news ignites his dangerous, barely suppressed Wraith instincts. As Ronon and a security contingent escort him to the infirmary for another treatment, he fights free of them and, before he's recaptured, kills a guard. Consequently, he's transferred under high security to the expedition's new Alpha site, a secondary base on another planet where Dr. Beckett can continue the experiment with less risk.
Beckett and Teyla both feel moral qualms about their actions - especially Teyla, who stays by Michael's side, convinced that he's good at heart. Her trust is put to the test, however, when he manages to break loose and escape with her as his hostage. Her life may now depend on Michael's human compassion - if, that is, he actually has any.