When SG-1 finds a vital clue in its search for the Lost City of the Ancients, Dr Weir prepares her team for a perilous journey under the sea.

Unable to return to Earth, the crew looks for a new fuel source. They happen upon a settlement, but the villagers live in fear, the enemy is coming.

The Atlantis base is threatened when the team discovers that an alien entity is in the city. McKay grows worried when he is unable to remove an Ancient shield device.

The team finds themselves in mortal danger when their Puddle Jumper ship becomes lodged in the Stargate.

After a series of run-ins with the Wraith, the team begins to suspect their Athosian allies of having a spy in their midst.

Sheppard and the team visit a world where no one is over 24 years old because of a ritual suicide practice they believe keeps the Wraith at bay.

The team finds a world whose people are on the brink of a discovery that may make them immune to the Wraith feeding.

Efforts to open trade relations with a species called the Genii turn sour when the team discovers their new "allies" have ulterior motives.

McKay's efforts to harness the energy of an alien planet's atmosphere allows for a return trip to Earth but the team may not be able to return to Atlantis.

When a massive storm threatens the city, Atlantis is evacuated only to be taken over by the team's newest enemy.

Major Sheppard plays a dangerous game of cat and mouse with soldiers who have seized control of Atlantis and taken Weir and McKay hostage.

Sheppard's team investigates a downed Wraith ship, and find themselves stuck on a planet with a lone Wraith survivor.

Nearly a third of Atlantis's residents are infected with a deadly virus that causes hallucinations and death, forcing a lockdown of the city.

The team finds a paradise world that would make an ideal sanctuary for those fleeing from the Wraith, but the local inhabitants believe their goddess will not permit it.

A woman is found in suspended animation in Atlantis, and the team is shocked to see that it is Dr. Weir herself, who tells them of her trip 10,000 years into the city's past.

The team searches for a valuable Zero Point Module rumored to be hidden on the planet Dagan but their new allies have motives of their own.

With a brief opportunity to send a data transmission to Earth, members of the Atlantis expedition compose video messages home to their loved ones.

Plagued by terrifying nightmares, Teyla begins to recall a time when she and her father were captured by the Wraith and subjected to disturbing experiments.

With a group of Wraith hive ships on the way to Atlantis, the team searches for a place to flee and a way to destroy the city. McKay leads a team to try and activate the Ancients' orbital weapons platform.

A new military contingent from Earth is sent to take command of Atlantis and defend it from the impending Wraith attack.