Waking up in a psychiatric hospital outside of Washington D.C., Dr. Elizabeth Weir is shocked to discover that her entire experience in Atlantis over the last two years was solely a figment of her imagination. Through the help of her psychiatrist Dr. Fletcher, she learns that a car accident that killed her fiancé left her in a near catatonic state and suffering from delusional psychosis.

Rodney McKay is called back to earth to convince his estranged sister, Jeannie Miller, to assist the Air Force in implementing an important mathematical proof that has application to one of McKay's experiments. Having not seen her in four years, McKay finds it difficult to pry Jeannie away from her family, so he has no choice but to disclose the existence of the Stargate program to her. McKay and Jeannie travel to Atlantis, and begin the experiment, which is intended to generate limitless energy by bridging parallel universes.