The third season of Stargate: Atlantis was a time of change for the series. The cast experienced several changes in the later part of the season, and the individual episodes focused more in this season on character development.
Ronon Dex is noticed by the villagers he once visited during his time as a runner. After getting turned in by the villagers to the Wraith, he is implanted with another Wraith tracker and dropped off on his abandoned homeworld, Sateda, where he is forced to become a runner again.
Dr.Rodney McKay gets "zapped" by a device, where his brain quickly evolves to that of the Ancients to achieve Ascension, and he gains super powers. However, he must learn to ascend, or he will die, but it isn't going to be easy.
MajorEvan Lorne reports back from M4D-058 and tells them they encountered a race of humans who has Dr.Rodney McKay's face on their flag. They learn that a game McKay and Lt. ColonelJohn Sheppard were playing is actually happening in reality. However, this also causes friction between McKay and Sheppard's worlds, who are on the brink of war.
Lt. ColonelJohn Sheppard's team discovers a Moon Base where the last of a race of humans remain. They soon discover, however, the entire population is in danger when the station is damaged through the suicide of a recently awoken resident.
While the Atlantis expedition tries and relax on a regular Sunday, a mysterious explosion rocks the city, leaving three people dead. It is later revealed that a scientist is a walking time-bomb, and has to be stopped. However, the attempt to resolve the problem will result in the loss of an important figure in Atlantis.
The new Earth battle-cruiser Apollo arrives in Atlantis to launch a preemptive strike against an armada of Asuran ships preparing to take off to Earth. However, after the strike is finished, a weapons satellite appears above the city and attacks its shields. If they cannot find away out of the situation, Atlantis will be no more.