Sheppard, McKay, Ronon and Caldwell return to Atlantis in triumph aboard their captured Wraith hive ship. Dr. Weir is on her way back from Earth as well, accompanied by the chief liaison to the International Oversight Advisory, Richard Woolsey, who is writing a report on Weir's suitability to command the expedition. His nagging questions and bureaucratic attitude are an annoyance as the Atlantis team struggles to decide the fate of the two hundred Wraith that they captured along with the hive.
Technically, these Wraith are not Wraith anymore. Dr. Beckett's weaponized retrovirus has stripped away both their memories and their alien genetic aspects, leaving only their human characteristics behind. Unfortunately, the effects of the retrovirus are temporary; if the former Wraith don't receive a new dose every day, they'll revert to their murderous former selves.
One additional Wraith has arrived at Atlantis with his memory intact: Michael. Teyla struggles to reason with the paranoid outcast, explaining that her teammates can't risk releasing him unless he takes Beckett's drug, too. When Michael angrily rejects her well-meant advice, Ronon and Beckett inject him with the retrovirus by force.
Sheppard and his team then transport all the former Wraith - including Michael - to a remote planet without a stargate. They tell the confused men that they must be quarantined because of a virulent plague that has caused their memory loss. Under this cover story, Beckett continues the daily injections. Against Sheppard's better judgment, in fact, the doctor insists on remaining on the planet with his unusual patients until a better solution can be found.
But Michael and a few others, suspicious of the story, secretly cease taking the medicine and regain their memories. When Sheppard's team leaves on a resupply mission, Michael seizes his chance. He and his fellow Wraith kill Beckett's security detail, capture the doctor, and interrogate him remorselessly before summoning a hive ship to come to their aid.
From Atlantis, Dr. McKay spots that ship on the city's long-range sensors. Weir orders Sheppard and his team to investigate, but the only ship available that can make the journey fast enough is the captured hive, and McKay can't figure out how to control its weapons. They might reach the planet safely, but once there they'll be sandwiched between the rebel Wraith below and the approaching Wraith ship above. Unless they can find a way to rescue Beckett and defend themselves, Woolsey's report to the I.O.A. will have an abrupt and tragic ending.