No Man's Land Sheppard's ship vanishes during a space melee against the Wraith. Meanwhile, Weir is recalled to Stargate Command as Colonel Caldwell leads a mission to keep the Wraith from reaching Earth.
Misbegotten Woolsey 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.
Irresistible The team searches for stargates to harvest for an intergalactic bridge, and encounters a charming alchemist who beguiles Dr. Beckett.
Sateda 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.
Progeny 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.
The Real World Dr. Weir has a rude awakening in a psychiatric hospital on Earth, where she is told that her memories of Atlantis are delusions.
Common Ground 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.
McKay And Mrs. Miller 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.
Phantoms 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.
The Return, Part 1 Ancients journey to Earth and request that the Stargate team vacate Atlantis, a scenario that scatters the team and presents General Landry with a quandary.
The Return, Part 2 The team tries to rescue General O'Neill and Richard Woolsey during the Asuran occupation of the outpost.
Echoes Teyla sees a strange woman in white aboard Atlantis as the sea creature that saved Rodney from the puddle jumper crash resurfaces, signaling a new threat to the outpost.
Irresponsible The team encounters Lucius, who uses Ancient technology to assume the role of protector for a besieged village.
The Tao Of Rodney Rodney is hit by an energy beam from an Ancient device and begins to exhibit heightened senses and telekinesis. The team discovers that the device was used to accelerate ascension, which may kill Rodney in the process.
The Game Sheppard and McKay compete in a real-time strategy game they've discovered on Atlantis, which may be more than a game.
The Ark Survivors are revived from suspended animation in a space station, but problems from their past come back to haunt the team.
Sunday Dr. Weir has an admirer in the form of a young scientist, which becomes awkward as an emergency situation unfolds on Atlantis.
Submersion An underwater mission has the team searching for an alternate power source in the Atlantean ocean.
Vengeance The team encounters an old enemy while searching for one of their allies, and uncovers a plot to engineer a race of powerful monsters.
First Strike The Apollo, a new Earth ship, arrives at Atlantis under the command of Colonel Abe Ellis, whose mission could start a war, and endanger the station in the process.