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After a conflict with Michael leaves several Atlantis personnel trapped, Colonel Carter leads a rescue mission.
When an alien organism incapacitates Dr. Keller, the team seeks help from an old friend recently revived from stasis.
Ronon once again comes face-to-face with Tyre, one of his people who became a Wraith worshiper -- but who now claims he has broken free of their influence.
The team boards the Daedalus when it shows up abandoned in orbit, only to find themselves skipping through parallel universes.
The city of Atlantis becomes host to the minds of disembodied Replicators, led by someone very close to the team.
Rodney McKay is stricken with a mental affliction that robs him of his knowledge and memories, causing him to revert to a childlike state.
Sheppard and Beckett join a team investigating a hidden Wraith laboratory where Michael has been conducting genetic experiments.
Teyla goes in disguise as a Wraith queen when Todd agrees to make a bold proposal to the leader of his alliance -- not realizing that he has other intentions.
Ronon and McKay join Dr. Keller on an off-world errand of mercy, and must track her through the forest when a Runner kidnaps her.
When Daniel Jackson visits Atlantis, he and Dr. McKay discover a hidden lab that brings a new enemy knocking. The Daedalus welcomes a Wraith ally for a special project.
Sheppard races to an Ancient laboratory to save McKay and Daniel Jackson before Todd arrives to destroy a weapon that has a devastating side-effect. Daniel uncovers the identity of the hostile new species.
The Wraith arrive in a village where Dr. Beckett is working, and demand that the locals turn over a group of refugees who survived the Hoffan plague -- or the entire village will be obliterated.
A new coalition of human worlds puts the Atlantis team on trial for their alleged crimes against the Pegasus Galaxy.
The team fights to retake control of Atlantis when Michael infiltrates the control room to take Teyla's child and destroy the city.
While being evaluated by the I.O.A. Richard Woolsey meets a beautiful scientist new to Atlantis, who is not what she appears. Sheppard is captured and tortured by an enemy he thought was dead.
Rodney returns to Earth with Jennifer to witness the triumph of his rival, who believes he has solved the problem of global warming. But when the new technology goes horribly awry, Rodney must help shut down the deadly weather device.
After Todd's hive ship shows up over Atlantis transmitting a distress call, the team discovers that he and his crew have been stricken with a disease they helped create.
Dr. Keller's body is taken over by a cunning thief, while Keller finds herself imprisoned with a death sentence on another planet.
In the city of Las Vegas, Detective John Sheppard must solve the case on a long string of unusual murders -- perpetrated by a Wraith in hiding.
The team learns that a rogue Wraith has acquired several Z.P.M.s to power a formidable new hive ship -- and he is headed for Earth.
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