Episode 20 - Enemy at the Gate 1/9/2009 Edit details "Enemy at the Gate"

Todd informs Atlantis that a rogue Wraith has acquired several Z.P.M.\'s to power a formidable new Hive ship. When the Daedalus engages it in battle but is unable to defeat it, the team gets a message indicating it is headed to Earth.

Episode 19 - Vegas 1/1/2009 Edit details Detective John Sheppard attempts to solve a string of unusual murders in Las Vegas.

Episode 18 - Identity 12/12/2008 Edit details "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.

Episode 17 - Infection 12/4/2008 Edit details The Atlantis team discovers that all the Wraith on board have placed themselves in stasis, the victims of a lethal affliction.

Episode 16 - Brain Storm 11/21/2008 Edit details "Brain Storm"

McKay returns to Earth to witness the unveiling of his rival's latest breakthrough.

Episode 15 - Remnants 11/13/2008 Edit details Once again, the city is threatened by an old enemy. This one's captured Sheppard and no one knows how it's all going to play out.

Episode 14 - The Prodigal 11/6/2008 Edit details An old foe, bent on revenge, infiltrates the Gate Room to take control of Atlantis. At the same time, Teyla and her infant son face a threat of deadly proportions.

Episode 13 - Inquisition 10/23/2008 Edit details Col. Sheppard and his team, aided by Dr. Beckett, struggle to save survivors of the Hoffan plague from being sacrificed to the Wraith.

Episode 12 - Outsiders 10/16/2008 Edit details Sheppard and his team are abducted by a newly formed galactic coalition and made to stand trial for crimes against humanity.

Episode 11 - The Lost Tribe 10/9/2008 Edit details With the Daedalus under siege, Dr. Daniel Jackson and Rodney McKay try to keep a reactivated Ancient weapon from triggering a cataclysmic chain of events.

Episode 10 - First Contact 9/25/2008 Edit details Atlantis encounters a mysterious alien race when Dr. Rodney McKay and a visiting Dr. Daniel Jackson stumble upon the secret lab of a rebellious Ancient scientist named Janus.

Episode 9 - Tracker 9/18/2008 Edit details Pursued by Hunter Wraith, only Ronon's skills as a former Runner can save a kidnapped Dr. Keller.

Episode 8 - The Queen 9/11/2008 Edit details Teyla risks her life on a daring mission aboard a Wraith hive ship.

Episode 7 - Whispers 9/4/2008 Edit details While exploring an abandoned catacomb on an unexplored planet, an Atlantis away team uncovers one of Michael's secret labs.

Episode 6 - The Shrine 8/21/2008 Edit details While on a rescue mission to another planet, Dr. Rodnet McKay falls fatally ill and his sister Jeannie is summoned from Earth to say her final goodbyes.

Episode 5 - Ghost in the Machine 8/14/2008 Edit details A mysterious entity causes crippling havoc within the city's computer system.

Episode 4 - The Daedalus Variations 7/31/2008 Edit details A drive malfunction aboard a mysterious duplicate Daedalus sends the team jumping thorugh various alternate realties where they encounter sinister alien life forms, a searing sun, and a pitched space battle over Atlantis.

Episode 3 - Broken Ties 7/24/2008 Edit details Ronon is captured by his former friend, Tyre, and turned over to the Wraith. As the team struggles for leads, Ronon goes on a torturous ordeal.

Episode 2 - The Seed 7/17/2008 Edit details When a mysterious alien organism takes Dr. Keller as it's host, Beckett and the crew deseperately search for a serum to save her from the evolving intruder before it can infiltrate Atlantis.

Episode 1 - Search and Rescue 7/10/2008 Edit details Atlantis races against time to save team members trapped in a collapsed compound, and rescue a pregnant Teyla from Michael's clutches.

Episode 20 - The Last Man 3/6/2008 Edit details Sheppard returns from another failed search for Teyla and finds Atlantis completely deserted.

Episode 12 - Spoils of War 1/10/2008 Edit details The Atlantis team successfully salvages a partially damaged Hive ship and in the process retrieve some critical information that many help their war against the Wraith.