The team learns that a storm of catastrophic proportions is headed straight for the city of Atlantis. Without enough energy to power the shields, Dr. Weir orders that Atlantis be evacuated until the storm passes. But Dr. McKay conceives of a last minute plan to save the city – harness the power of the electrical storm to fuel the shields. Meanwhile, unbeknownst to the Atlantis team, the Genii have learned of Atlantis' evacuation, and devise a dangerous plan to take over the city's weapons for themselves. With Weir and McKay taken hostage and Lt. Ford and Teyla aiding the evacuees, it is up to Major Sheppard to shut down the remaining grounding stations and save Atlantis from invasion before the storm hits.

Leading an exploration of an ancient weapons satellite in deep space, Major Sheppard and Dr. McKay intercept a Wraith distress signal. Deciding to investigate, the team lands on a nearby planet and finds the source of the call - a downed Wraith cargo ship. When the unseen Wraith awakens from hibernation, Sheppard and McKay become the focus of its ravenous appetite.