Season 5 premieres. A race against time pits Col. Carter's crew against Michael and his Wraith hybrids to recover the Atlantis team trapped in the rubble of Michael's facility.

Dr. Carson Beckett (Paul McGillion) is revived from the stasis chamber after an alien organism incapacitates Dr. Keller and triggers a quarantine of the Atlantis team.

Ronon endures a grueling ordeal after his former friend, Tyre (Mark Dacascos), captures and delivers him to the Wraith. Meanwhile, the team launches a rescue mission for their missing comrade.

The team becomes trapped on a runaway duplicate of the Daedalus, which takes them to numerous alternate realities.

A puddle-jumper mishap leads to a series of Atlantis power disruptions, which are linked to a former ally.

Dr. Rodney McKay faces death in the form of a fatal illness, leading to the depletion of his memories, behavioral regression and a trip to a special shrine.

After discovering one of Michael's secret labs, the team investigates the abandoned village near the facility.

After Dr. Keller comes to believe she can cure the Wraith of their need to feed on humans, Teyla embarks on a undercover mission with the help of Todd, the team's Wraith ally.

Dr. Keller vanishes during a medical mission, forcing Ronon to tap into his past experiences to try to save her.

Dr. Daniel Jackson (Michael Shanks) visits Atlantis and enlists Dr. McKay's help to find a hidden lab on the station. Meanwhile, the Daedalus hosts a Wraith delegation for talks concerning Dr. Keller's research.