Season synopsis
Contains spoilers for this season and earlier seasons.
The Daedalus arrives in time to beam Sheppard away from his suicide bombing run and deliver a new Zero Point Module. The expedition defeats the first Wraith assault, then hides Atlantis behind a cloak while a nuclear blast makes a larger fleet believe the city has destroyed itself. Ford survives the siege, but exposure to Wraith enzyme leaves him paranoid and dependent on it. He escapes Atlantis in a stolen Jumper, and later encounters with his enzyme-using followers fail to bring him home.
The expedition's search for people and power brings Sheppard's team into contact with Ronon Dex, a former Satedan soldier hunted by the Wraith. Ronon joins Atlantis after Beckett removes the tracker embedded in his back. Meanwhile, Beckett develops a retrovirus intended to strip Wraith of their feeding biology, and the team tests it on Michael, a captive who believes himself human until he discovers what was done to him. The experiment gives the expedition a possible weapon while making its ethical cost personal.
Earth contact becomes possible again, often through the Daedalus, but the expedition has to hide Atlantis from new allies as well as enemies. The Genii bargain over power and territory, while the team finds that the Wraith are fighting among themselves after awakening in numbers too large for the available human population. In the finale, a Wraith faction that includes Michael proposes using the retrovirus against rival hives; the alliance is a trap, and the Wraith obtain information that points them toward Earth, setting up the next attack.