While collecting artifacts on a distant planet, Daniel Jackson is knocked out after touching a mirror-like object. He awakens in the same room but is unable to locate the other members of SG-1. Assuming that they left without him, he dials up his return home but gets there to find that he is in a different reality. In this world, General Jack O'Neill and Catherine Langford are in charge of the Stargate program; Hammond is a Colonel reporting to O'Neill; and Sam Carter is a civilian scientist working on the project (and also engaged to O'Neill). More importantly, Earth is under attack from the Goa'uld who have already killed over 1 billion people. Carter believes that somehow, Jackson is from a parallel dimension. When Jackson learns the point of origin of the Goa'uld attack, he wants to return to his own universe, believing that his Earth will be similarly attacked.

Sam's father hopes that SG-1 can help find and neutralize Seth, an Ancient Goa'uld who the Tok'Ra believe may still be hiding on Earth after thousands of years.