In the aftermath of the self-destruct of Michael's compound, Sam leads a team to rescue the survivors. Sheppard, Ronon and McKay must then rescue Teyla from Michael's cruiser as she goes into labor.
The Atlantis team is under a quarantine after Dr. Keller is incapacitated by an alien organism, and a recently revived Dr. Beckett is put in charge of the investigation.
Tyre, Ronon's former Satedan comrade, captures Ronon and turns him over to the Wraith. As the Wraith drain Ronon in an attempt to turn him into a Wraith worshiper, the Atlantis team struggle to find their comrade. Meanwhile Teyla reconsiders her role on the team after the birth of her child.
The team is sent through a series of deadly alternate realities caused by a drive malfunction aboard a mysterious duplicate Daedalus, in which they encounter sinister alien lifeforms, a searing sun, and a space battle for Atlantis.
When Sheppard's team returns from a mission, a strange electrical surge spreads from their Jumper to Atlantis' systems. It spreads, and the team soon discovers that an old teammate is responsible.
McKay starts to suffer from the onset of senility to an Alzheimer's-like disease.
While investigating one of Michael's facilities, a hybrid creature attacks Sheppard and Beckett.
The Atlantis team is forced to ally with their Wraith contact again when he negotiates an alliance with another Hive.
Ronon and McKay have to find a kidnapped Keller, who is abducted to help a village threatened by the Wraith. However, they soon discover that the kidnapper is a Runner.
Daniel Jackson arrives on Atlantis on a research mission to locate Janus' laboratory. However, its discovery triggers off an alien invasion and the possible destruction of the Wraith.
When Daniel Jackson and McKay are trapped in an Ancients lab, Sheppard and the others must get there before Todd the Wraith does.
Sheppard and his team try to evacuate a group of Michael's test subjects before the Wraith find and destroy them.
Sheppard's team is captured by a new coalition of Pegasus Galaxy civilizations, and must defend Atlantis against accusations that they have killed millions due to their arrogance.
Michael returns and is intent on recovering Teyla's baby to further his experimentation... and will go to any lengths to obtain him.
While exploring the mainland, John encounters an old enemy out for revenge. Meanwhile, the IOA sends someone to review Woolsey's performance, and Rodney and Zelenka discover an alien device on the ocean bottom.
Rodney reluctantly returns to Earth with Keller to watch the unveiling of his rival's new weather device, but when it goes awry, he's the only one who can stop it.
After a Wraith hive ship shows up over Atlantis transmitting a distress call, a team investigates and finds that its crew have been stricken with a familiar disease.
An alien thief, Neeva Casol, inadvertently uses an Ancient device to switch minds with Dr. Keller from a distance. While she deals with the team on Atlantis, Keller must handle Neeva's uninformed accomplices.
Detective John Sheppard works a serial killer's case in Las Vegas, but a stranger informs him reality isn't all that it seems.
Todd brings Atlantis news that one of his underlings has obtained a ZPM, and plans to use it to build a new Hive supership... and attack Earth.