Search And Rescue A race against time pits Colonel Carter's crew against Michael and his Wraith hybrids to recover the Atlantis team trapped in the rubble of Michael's facility.
The Seed Dr. Carson Beckett is revived from the stasis chamber after an alien organism incapacitates Dr. Keller and triggers a quarantine of the Atlantis team.
Broken Ties Ronon endures a grueling ordeal after his former friend, Tyre, captures and delivers him to the Wraith. Meanwhile, the team launches a rescue mission for their missing comrade.
The Daedalus Variations The team becomes trapped on a runaway duplicate of the Daedalus, which takes them to numerous alternate realities.
Ghost In The Machine A puddle-jumper mishap leads to a series of Atlantis power disruptions, which are linked to a former ally.
The Shrine 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.
Whispers After discovering one of Michael's secret labs, the team investigates the abandoned village near the facility.
The Queen 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.
Tracker Dr. Keller vanishes during a medical mission, forcing Ronon to tap into his past experiences to try to save her.
First Contact Dr. Daniel Jackson 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.
The Lost Tribe Rodney and Daniel activate an Ancient weapon before determining its threat to active stargates; Todd's group continues to hold the Daedalus crew captive.
Inquisition Sheppard's team is seized and detained by an interplanetary council that wants to try them for crimes against the people of the Pegasus Galaxy, prompting Woolsey to intervene.
Outsiders Refugees are imperiled when the Wraith threaten to destroy their village sanctuary, forcing Sheppard and Beckett to intervene.
The Prodigal An old foe usurps Atlantis by breaching the Gate Room, forcing McKay and Sheppard to make an arduous climb while a scheme involving Teyla's son unfolds.
Remnants Woolsey faces an uncertain future in the form of a performance evaluation; Zelenka and McKay examine an object discovered on the ocean floor; Sheppard encounters an ambush.
Brain Storm Doctors Keller and McKay go to Earth to witness a scientific demonstration conducted by McKay's rival, Malcolm Tunney. Unfortunately, Tunney's device creates a life-threatening situation.
Infection A distress call from a hive ship over Atlantis leads the team to discover a Wraith crew in stasis, with all hands stricken with a disease caused in part by Dr. Keller's gene therapy.
Identity Dr. Keller suffers the ultimate form of identity theft when her strange behavior leads the team to discover that her consciousness has been switched with that of a criminal who is facing capital punishment.
Vegas Detective John Sheppard investigates murders in Las Vegas linked to an unusual man with superhuman abilities.
Enemy At The Gate Todd warns Atlantis about a sophisticated hive ship and encourages the team to attack the vessel before it can pose a threat to Earth.