The team meets a man with extraordinary prophetic abilities, who gives them a dark prediction about Atlantis' future. Meanwhile, they join forces with a Wraith in an attempt to fix the virus Rodney created earlier to stop the Replicators, that has since malfunctioned. Woolsey arrives at Atlantis to conduct an evaluation of Carter's command.
During a visit to New Athos, Teyla and Dr. Keller find themselves on the run from a primitive tribe of warriors and Teyla makes a shocking discovery.
When a deadly infection causes key members of Atlantis to lose their memories, it's up to Teyla and Ronon to find a cure. But when the Marines begin hunting down everyone and no one remembers why, it's hard to work together to cure everyone.
Sheppard is captured by a space-faring race who wish to use his Ancient gene for their own ends.
After discovering a crystal entity, the team begins to have nightmares involving Sheppard.
Ronon is reunited with a group of his fellow Satedans who ask him to leave Atlantis and join them. Colonel Samantha Carter arrives at Atlantis to assume command.
While Carter and the Apollo search for missing city of Atlantis, Sheppard and his team risk their lives on a mission to steal a Z.P.M. from the Replicators.
With only 24 hours of power left, and unable to use the Stargate, the Atlantis team must once again save the city from certain doom, while Dr. Weir struggles to survive.
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.
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.