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.

Dr. Rodney McKay undergoes experimental gene therapy, altering his DNA to match the Ancient genetic coding. The experiment opens up countless scientific possibilities, as well as an unexpected problem. Meanwhile, during a game of hide and seek, one of the Athosian children inadvertently opens a containment unit that lets loose a seemingly harmless black ethereal cloud. But when Atlantis goes through a series of technical malfunctions, they realize that the shadowy creature is actually feeding off of the power supply!