Teyla is haunted by nightmares, leaving her agitated. After seeing a psychologist, an old Athosian woman tells her a secret about her ability to sense the Wraith.

The Daedalus arrives and the two hive ships are destroyed. Atlantis seems saved, then Zelenka detects 12 more ships. Ford seems changed after a fall in the water.

The team discovers a planet where the Stargate is kept on a prison island to keep the Wraith satisfied. Their magistrate is willing to trade a rare mineral.

Sheppard is infected with the Wraith retrovirus and slowly turns into an Iratus bug. To provide a treatment, stem cells must be retrieved from one of their eggs.

Sheppard and the others are now in control of the one remaining hive ship with most of the Wraith transformed into human form, courtesy of the retrovirus. They do learn something interesting about female Wraiths, however. After they return to Atlantis, the question becomes one of what to do with the Wraiths who are again human, especially Michael who has proved to be quite helpful. Elizabeth Weir meanwhile is surprised to hear that she is to return to Atlantis as the expedition leader. She will be accompanied however by Richard Woolsey who is to review her leadership and make recommendations to the International Oversight Advisory on whether she should be allowed to continue.

After a group of people capture and give Ronon to the Wraith, he becomes a runner again, but this time he's left in his home planet, Sateda, where the Stargate has been disabled.

The Atlantis expedition encounters a highly advanced race, the Asurans. They initially believe them to be the Ancients. However, this new race is just a new face of an old nemesis.

After learning the Asurians are building a fleet of ships, Earth sends its newest ship, the Apollo, under the command of Colonel Abe Ellis to initiate a preemptive first strike to stop them from attacking Atlantis or worse, Earth itself.

With a damaged ZPM, and diminished hopes of survival, the Atlantis team finds themselves stranded in the middle of empty space with hardly any time before they run out of power completely. Dr. McKay is challenged to the max as he tries to find a way to save Atlantis from its doom. Meanwhile, Dr. Keller races to treat Weir's increasing head injuries, but the only answer she can come up with could have grave results for everyone on board.

Dr. Carson Beckett is removed from stasis because he's the only one who can find the antidote to a mysterious virus that has incapacitated base personnel, beginning with Dr. Jennifer Keller.