The Stargate SG-1 team discovers what they believe to be the remnants of the lost city of the Ancients – the originators of the Stargates and Stargate Command launches an investigation to find the mythical city of Atlantis. Situated in the distant Pegasus Galaxy, it's farther than any Stargate team has ever traveled. With only enough power to make a one-way trip, a new team, headed by civilian Dr. Elizabeth Weir, is formed and travels through the gate to this unknown galaxy. There, they discover the marvels of the lost city of Atlantis.... and encounter a sinister new enemy.

Fleeing from a surprise encounter with the Wraith, Major Sheppard falls victim to an alien symbiote which is feeding off his life force and slowly paralyzing him. While speeding back to Atlantis for medical aid, the team gets trapped halfway through the Stargate when the puddle jumper, damaged in the altercation with the Wraith, suffers a mechanical failure. With only thirty-eight minutes before the Stargate shuts down, Lieutenant Ford and Dr. McKay struggle to manually fix the problem. As the clock ticks away, the Atlantis team must come together, or perish in the harsh vacuum of space.