Season three of Stargate: Atlantis gets underway as the temporary alliance between the Atlantis team and the Wraith breaks down, and the Wraith hive ships prepare to launch a devastating attack on planet Earth. Before returning to Earth to stand accountable for the failure of her team, Weir (Tori Higginson) orders Colonel Caldwell (Mitch Pileggi) to destroy the Hive ships using the Orion and the Daedalus. Meanwhile, Sheppard (Joe Flanigan) has latched his F-302 to the hull of a Wraith ship and must now rely on Michael (Connor Trinneer) if he hopes to rescue Ronon (Jason Momoa) and McKay (David Hewlett) from the vengeful wraith. As the imprisoned pair miraculously break free of their cocoon prisons and hatch a dangerous plan to sabotage the Wraith ship, the Orion and the Daedalus speed through space to engage the Hive ships in a decisive space battle that could determine the fate of an entire planet.

Woolsey (Robert Picardo) travels to Atlantis to evaluate Dr. Weir's leadership. Meanwhile, Dr. Beckett and Sheppard are at odds over what to do with the former Wraith transformed into humans by the retrovirus. Michael: Connor Trinneer.

The team searches for stargates to harvest for an intergalactic bridge, and encounters a charming alchemist who beguiles Dr. Beckett. Lucius: Richard Kind.

While on an exploratory mission, Ronon is taken prisoner by villagers who made a pact with the Wraith. Meanwhile, Sheppard and Teyla rally the team to rescue their comrade.

An advanced civilization is accidentally discovered during the team's investigation of a purportedly abandoned Ancient testing site, prompting Weir to broker an alliance with the society's leader, Oberoth (David Ogden Stiers).

Dr. Weir has a rude awakening in a psychiatric hospital on Earth, where she is told that her memories of Atlantis are delusions. Richard Dean Anderson reprises his "Stargate SG-1" role as Gen. Jack O'Neill.

Sheppard is captured by a Genii commander and imprisoned beside a Wraith, who becomes a tool in negotiations to release Sheppard, as well as an unlikely ally, for his escape. Kolya: Robert Davi.

McKay returns to earth to enlist his sister's help in solving problems concerning an Air Force experiment to generate energy, which produces a surprise visitor. Jeannie Miller: Kate Hewlett.

A mission to recover a lost team leads to the discovery of a discontinued Wraith experiment: a mind-altering device that adversely affects Ronon and Sheppard.

Part 1 of two. Ancients journey to Earth and request that the Stargate team vacate Atlantis, a scenario that scatters the team and presents Gen. Landry (Beau Bridges) with a quandary. Gen. O'Neill: Richard Dean Anderson. Richard Woolsey: Robert Picardo.