Season synopsis
Contains spoilers for this season and earlier seasons.
Elizabeth Weir leads an international expedition through the Stargate to the lost city of Atlantis, deep in the Pegasus Galaxy. The team includes military officer John Sheppard, scientist Rodney McKay, physician Carson Beckett and Aiden Ford; they soon meet Teyla Emmagan and the Athosians, whose knowledge of local worlds helps the newcomers make contact with other human communities. Their early missions expose them to the Wraith, who feed on humans and begin emerging from hibernation.
The expedition searches for power, allies and a way to keep the Wraith from finding Atlantis. Its encounters force Weir and Sheppard to weigh help against interference: the Genii present themselves as less advanced farmers before the team discovers their underground weapons program, while Beckett and McKay test Ancient systems and medical ideas. A vast storm later threatens the city as Genii commander Kolya takes advantage of the evacuation to seize it; Sheppard's team and people left behind work together to retake Atlantis before the storm arrives.
When a Wraith fleet closes in, the team tries to activate an Ancient orbital weapon, but it destroys only one hive ship and kills scientist Peter Grodin. Weir orders the city evacuated and starts its self-destruct, then Earth sends reinforcements through the gate and promises a Zero Point Module aboard the Daedalus. Colonel Everett takes command as the Wraith attack; Sheppard launches a Puddle Jumper carrying a nuclear weapon toward a hive ship, leaving the battle unresolved at the season break.