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.
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....
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.
While investigating reports of a "superhero" on another planet, Colonel Sheppard's team comes across two old acquaintances.
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?
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.
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.
Sheppard and Ronon find themselves under the influence of a Wraith mind-altering device that threatens to force the entire team to kill--each other!
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.
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.