Two Wraith Hive ships have captured Dr. McKay and Ronon and are on their way to Earth. It is up to Colonel Sheppard to rescue them and figure out a way to stop the Wraith from reaching a "new feeding ground".
After turning a Wraith hive ship crew into humans, the Atlantis team must decide on their fate. Meanwhile, Dr. Weir finds herself under the scrutiny of Richard Woolsey and the I.O.A.
A man from another world has an unusual effect on the Atlantis team, causing them to behave strangely. The few unaffected team members must uncover the cause.
Sheppard, Teyla and Ronon come under attack on a forested world. Ronon, realizing that he has been on the planet before, learns that his earlier visit came with harsh consequences.
Dr. Weir accompanies Sheppard's team on a mission to an advanced civilization with a past history with Atlantis. They uncover a connection to an earlier discovery in the city.
Dr. Weir awakes in a sanitarium outside Washington, D.C., and is told that Atlantis and the Stargate program exist only in her mind.
John Sheppard is captured by the evil Kolya of the Genii and imprisoned in a cell adjacent to a Wraith as Dr. Weir negotiates for his release.
When his sister Jeannie comes up with a vital mathematical proof, Rodney returns to Earth to take her back with him to Atlantis. But things become complicated when another Rodney McKay from a parallel universe arrives.
Sheppard and Ronon find themselves under the influence of a Wraith mind-altering device that threatens to force the entire team to hug--each other!
While testing a chain of Stargates that will allow travel from Atlantis to Earth in about 30 minutes (the "McKay-Carter Intergalactic Gate Bridge"), McKay, Sheppard and the team discover an Ancient ship traveling at almost the speed of light.
When Dr. Weir talks to the travelers, she is surprised by their request that the expedition members vacate the city of Atlantis.
Major General Jack O'Neill's mission to defend Atlantis fails as he and Richard Woolsey are taken prisoner during a Replicator assault on the city. Sheppard's team, Dr. Weir and Dr. Carson steal a Jumper from Stargate Command on Earth and come back to Pegasus galaxy with a plan to retake Atlantis.
The whales of Lantea congregate around the city and the inhabitants of Atlantis begin to suffer ill effects. Are they there to communicate or attack?
While investigating reports of a "superhero" on another planet, Colonel Sheppard's team comes across two old acquaintances.
While shutting down unnecessary systems in Atlantis, McKay is zapped by a strange Ancient machine. He begins to have superpowers, but things are never as they seem, and Rodney and the team must race against his mutations to save his life.
To while away the hours, Sheppard and McKay have been secretly competing against one another in a real-time strategy game they discovered on Atlantis. To their surprise, they discover that this is more than just a game....
The Atlantis team uncovers the last survivors of a civilization who have been placed in suspended animation aboard a space station. As some of the people awaken, problems from the past threaten to destroy everyone on the station, including Sheppard.
The team tries to relax during a mandatory day off until the city and the Expedition are devastated by explosions.
The team goes searching for an alternate power source beneath the surface of the Lantean ocean. When arriving at the power plant, Teyla senses a Wraith nearby.
When Atlantis loses contact with the Taranian settlement Sheppard's team goes to investigate and finds that Michael has been doing experiments on them involving the Iratus bug.
Colonel Abe Ellis arrives at Atlantis with a new Earth ship, The Apollo and a new mission. Dr. Weir has misgivings about that mission, one that could start a war with a very powerful enemy. When his mission goes wrong, Weir must take radical action to save Atlantis.