Rising, Part 1 Dr. Weir lobbies Brigadier General O'Neill to allow her team to seek the underwater city on a faraway planet despite O'Neill's misgivings about their chances of returning to Earth.
Rising, Part 2 Cut off from Earth and menaced by the mysterious Wraith, Weir and Sheppard turn to McKay to harness the technology of Atlantis to safeguard the city and protect their team's new allies, the Athosians.
Hide And Seek McKay is trapped in a force field after altering his genes to access the Ancients' technology, and the city is rocked by systems malfunctions after a child unwittingly releases an eerie black cloud.
Thirty-Eight Minutes While fleeing from a Wraith ambush, the crew is endangered when the puddle jumper becomes lodged in the Stargate with only 38 minutes of life support available. Also, Major Sheppard is paralyzed by an alien symbiote.
Suspicion When the Atlantis team is bushwacked by the Wraith, Dr. Weir suspects a spy is lurking among the Athosians, who resent being relocated on the basis of mere accusation.
Childhood's End Members of the team must make an emergency landing on a planet populated entirely by young people who willingly die in a mystic rite to protect their civilization from the Wraith.
Poisoning The Well The team discovers another planet preyed on by the Wraith - only here, the locals have been developing a drug to protect themselves from their tormentors.
Underground The team establishes contact with the Genii, an agricultural collective whose eagerness to establish relations with Atlantis belies its true agenda.
Home The team uncovers a way to travel to Earth, but after reporting the progress to General Hammond, the team learns it may not be able to return to Atlantis.
The Storm The approach of a powerful storm prompts Weir to order the evacuation of Atlantis, which gives a new enemy the opportunity to move in and claim its abandoned resources.
The Eye With Kolya and his minions in control of Atlantis, Sheppard uses his knowledge of the city to strike back from the shadows as Weir and McKay await rescue.
The Defiant One Weir dispatches Sheppard, McKay and two scientists to locate and probe a downed Wraith ship, unaware they're like manna from Heaven to a surviving passenger.
Hot Zone The team issues a citywide quarantine when several residents of Atlantis are infected with a deadly nanite virus.
Sanctuary The Atlantis team discovers a utopia that may provide protection from the Wraith, but the civilization's high priestess believes their goddess will not allow outsiders.
Before I Sleep The team discovers that a woman who has been kept in suspended animation for 10,000 years is none other than Dr. Weir, who recalls her journey into the city's past.
The Brotherhood The team arrives on the planet Dagan, where the natives assist their search for the Potentia - a module that could power Atlantis, including a shield that protects the city from the Wraith - but their mission is obstructed by the Daganite agenda. McKay, meanwhile, is puzzled by a local woman's attention.
Letters From Pegasus Members of the Atlantis team prepare videos for their friends and families when conditions allow for the chance to send messages to Earth.
The Gift A series of nightmares jump-starts Teyla's dormant memory of an incident in which she and her father were subjected to terrifying experiments by the Wraith.
The Siege, Part 1 As a fleet of Wraith hive ships approach Atlantis, Sheppard and Weir consider drastic action to prevent their foes from occupying the city as McKay jury-rigs the Ancients' defense technology.
The Siege, Part 2 As Weir prepares to destroy the city to prevent a Wraith takeover, Earth reinforcements arrive to relieve the team, determined to defend Atlantis to the last man.