Six months after the Athosian people - including Kanaan, the father of Teyla's unborn child - vanished, Teyla has several visions in which Kanaan begs her to find him. He hints that she can pick up his trail in a village called Croya, but when Teyla, Sheppard, McKay and Ronon search it, they can't find any trace of the Athosians.
All too soon, the team - minus Teyla, who stays in Atlantis - hurries back to Atlantis because Col. Carter needs their help with another problem. An illness is spreading through the galaxy, killing 30 percent of the humans it infects. It is derived from a protein created several years earlier by the Hoffan people, who were trying to make humans toxic to the Wraith.
Sheppard's team investigates the planet Hoff, which was devastated by the Wraith after they learned of the Hoffans' intentions. McKay discovers that all information about the protein is missing from Hoff's ruined archives. Someone has stolen it to resume the project, not caring that the protein turned out to be fatal to humans as well as Wraith. As the team returns with this news to Atlantis, Todd, their occasional Wraith ally, signals that he wants to meet. Sheppard's team travels to a rendezvous point to discuss the mysterious illness with him.
Meanwhile, Teyla has another vision in which Kanaan begs her to investigate Croya more carefully. Returning to the planet with Lorne's team, she discovers a man selling Athosian jewelry, but as she pursues this lead, a Wraith dart suddenly swoops in and beams her up. The entire thing was a setup.
Imprisoned aboard a Wraith ship, Teyla meets her captor: Michael, the human-Wraith hybrid who hates both species. He - not Kanaan - sent the visions to her as bait. He is also behind the disease that's sweeping the galaxy. Furthermore, he took the Athosians captive in order to turn them into dronelike human-Wraith hybrids. With these hybrids as his army, he plans to wipe out the Wraith and become the galaxy's dominant power. To Teyla's horror, he introduces her to Kanaan, now transformed into his loyal minion.
With Todd's help, Sheppard's team pinpoints a Wraith base where Michael might be holding Teyla. Joined by Lorne and his men, they fly to the planet aboard the Daedalus and raid the base, facing stiff resistance from its guards.
Then a Wraith ship en route to the planet arrives in orbit, exchanges fire with the Daedalus, and flees. A guard on the planet reveals that Teyla and Michael were aboard that ship. Sheppard is frustrated to have lost them, but then Lorne calls his attention to a locked cell. The base already houses an important prisoner, and Sheppard, McKay, Ronon and Lorne are shocked to discover who it is...