With changes in leadership and new allies, the team continues to battle the Wraith and confront new existential threats. Personal dynamics shift as members struggle with loss and make significant choices that shape the fate of Atlantis and its mission in the Pegasus Galaxy.
Episode 1
Adrift (2)
Sep 27, 2007
Floating in deep space with the city's protective shield failing, the team must do all they can to keep Atlantis alive. A radical injury threatens Dr. Weir's life.
Episode 2
Lifeline (3)
Oct 4, 2007
Colonel Sheppard and his team embark on a risky mission to steal a Z.P.M. power module from the Replicators -- but must rely on a compromised Dr. Weir to succeed.
Episode 3
Reunion
Oct 11, 2007
When a group of Ronon's people enlist the team's help in raiding a Wraith weapons facility, Ronon reconsiders whether his future lies in Atlantis or with his friends.
Episode 4
Doppelganger
Oct 18, 2007
During an off-world mission Colonel Sheppard unknowingly becomes host to an alien entity, which infects others in Atlantis and afflicts them with terrifying nightmares.
Episode 5
Travelers
Oct 25, 2007
Colonel Sheppard is captured by the inhabitants of a generational ship and their beautiful leader, who wish to use his ability to use Ancient technology for their own ends.
Episode 6
Tabula Rasa
Nov 1, 2007
When a virus causes amnesia in everyone except Teyla and Ronon, the Atlantis team must work together to find a cure before their memories fade entirely.
Episode 7
Missing
Nov 8, 2007
During a visit to New Athos, Teyla and Dr. Keller find themselves on the run from a primitive tribe of warriors.
Episode 8
The Seer
Nov 15, 2007
The team meets a man with extraordinary prophetic abilities, who gives them a dark prediction about Atlantis's future. The Wraith seek a new alliance with Atlantis in their war with the Replicators.
Episode 9
Miller's Crossing
Nov 29, 2007
Rodney McKay goes in search of his sister on Earth after she is kidnapped by the head of a powerful corporation.
Episode 10
This Mortal Coil (1)
Dec 6, 2007
A mysterious drone crashes into Atlantis, indicating that the Replicators may have found the city. But when Elizabeth Weir appears, the team realizes that the probe is just a part of a bigger mystery.
Episode 11
Be All My Sins Remember'd (2)
Jan 3, 2008
With a plan to potentially extinguish the Replicator threat, the Atlantis team must seek an alliance with a fleet of Wraith ships.
Episode 12
Spoils of War
Jan 10, 2008
The team finds their former Wraith ally's hive ship drifting in space, which leads them to a secret project that could turn the tide of a civil war.
Episode 13
Quarantine
Jan 17, 2008
An automated lockdown traps Atlantis personnel in various parts of the city, each of them hoping the others will come to their rescue.
Episode 14
Harmony
Jan 24, 2008
Colonel Sheppard and Dr. McKay must protect a child princess on a pilgrimage before she can become queen, and learn that she has dangerous enemies threatening her life.
Episode 15
Outcast
Jan 31, 2008
While on personal leave on Earth, Sheppard and Ronon learn that scientists have engineered a human-form Replicator -- who is now on the loose.
Episode 16
Trio
Feb 7, 2008
McKay, Carter, and Keller are trapped in an underground chamber while on an off-world mission, with no apparent means of escape.
Episode 17
Midway
Feb 14, 2008
Teal'c visits Atlantis to counsel a headstrong Ronon, who is up for review by the I.O.A. But the two must work together when the Wraith invade the Midway space station in order to reach Earth.
Episode 18
The Kindred (1)
Feb 21, 2008
As a mysterious new illness sweeps through the Pegasus Galaxy, Teyla is convinced by a vision that the father of her child is trying to communicate with her.
Episode 19
The Kindred (2)
Feb 28, 2008
The team is shocked when an old friend, believed to be dead, miraculously returns to them. Teyla plans an escape from Michael's captivity.
Episode 20
The Last Man (1)
Mar 6, 2008
Sheppard returns to Atlantis after a mission and finds the city abandoned, all systems dead -- and instead of ocean, sand dunes as far as the eye can see.