Season synopsis
Contains spoilers for this season and earlier seasons.
The season opens with two Wraith hive ships heading for Earth after their alliance with Atlantis collapses. Sheppard tries to rescue the captured McKay and Ronon while the Daedalus and Ancient warship Orion try to stop the ships; the expedition uses Beckett's retrovirus to turn Wraith into humans, disrupting the attack but leaving a colony whose members must face what they have become. Back in Atlantis, Weir returns to command under review by Richard Woolsey, while Michael's anger over the experiment grows into a lasting threat.
The team encounters the Asurans, human-shaped Replicators who claim to be descended from the Ancients, and discovers diplomacy cannot prevent them from targeting Atlantis. After the Ancients reclaim the city and then lose it to the Asurans, Sheppard and his team return with Beckett, Teyla and Ronon to rescue O'Neill and Woolsey and retake the base. Other missions expose how the expedition's choices can disrupt local lives, from Sheppard and McKay's game that pushes two societies toward war to Teyla's dangerous effort to learn more about the Wraith.
On a day off, an explosion reveals an Ancient device has left scientists with lethal tumors; Beckett removes an explosive tumor from a patient, but dies when it detonates as he tries to dispose of it. His body is returned to Earth, and McKay must tell his mother what happened. The finale begins with the Apollo striking an Asuran base, but a satellite weapon answers with a beam that batters Atlantis. The city escapes by activating its stardrive, yet is left adrift in space with failing power, while Weir is critically injured in the attack.