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.

While testing the new McKay-Carter intergalactic gate bridge, the Daedalus detects an Ancient Atlantian warship, traveling at just below light speed and heading towards Earth. Damaged in battle during the war with the Wraith, the Ancients aboard this ship fled the Pegasus galaxy and have spent thousands of years in stasis. Back on Atlantis, the now awoken Ancients meet with General O'Neill and Richard Woolsey. They thank the Stargate team for taking care of the city in their absence, but ask them to vacate Atlantis immediately.