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 (Torri Higginson) 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.

A new Stargate team embarks on a dangerous mission to a distant galaxy , where they discover a mythical lost city -- and a deadly new enemy. Part 2 of 2.

Dr. Rodney McKay (David Hewlett) 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!

Fleeing from a surprise encounter with the Wraith Major Sheppard (Joe Flanigan) 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 (Rainbow Sun Francks) and Dr. McKay (David Hewlett) 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.

Relationships are torn part when the Athosians are accused of harbouring a spy.

During an exploratory mission the puddle jumper’s electrical systems are knocked out by a massive electromagnetic field and the team is forced to make an emergency landing. They soon encounter a primitive tribe of children who have been untouched by the Wraith for centuries due to the protective force of the electromagnetic field. But the children believe it is their ritual of mandatory suicide at the age of 25 that keeps the enemy at bay despite the contrary insistence of the Atlantis team. Fearing the “full growns” in their midst will attract the Wraith the villagers become anxious for their unexpected guests to leave as soon as possible. But to be able to leave Dr. McKay (David Hewlett) must first disable the electromagnetic field. In doing so he unwittingly trips a Wraith silent alarm leaving the tribe open to attack.