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.

While redialing old Stargate addresses, the SGC discovers that a gate that was previously buried has become uncovered. They send a probe through and find two archaeologists. However, when they travel through the Stargate, they find that it is located in a society in civil war: one continent believes that the people were created by a Goa'uld, whilst their enemy believes that humans arrived from another planet - by the Stargate. O'Neill, Carter and Jackson are captured by the authorities and questioned, but Teal'c is wounded and blinded. Can he help SG-1 escape the hostiles and get back through the Stargate?

General Hammond mysteriously retires from the SGC and a new general is brought in, who breaks up SG-1: Daniel and Sam are scientists, Teal'c is with SG-3 and O'Neill commands a new SG-1. O'Neill tries to convince Gen. Hammond to return, but he finds out that someone ordered Hammond to leave or they would hurt his grandchildren. While the others are occupying the new general, O'Neill tries to find out who that "someone" is. Thereto he must place his trust in the one person he hates most: Maybourne.

In a firefight with Jaffa, Teal'c takes a staff blast to the gut. Without his symbiote, he cannot regenerate as he once did. Daniel feels that he cannot remember something important, so he goes searching through the logs for any sign of his lost knowledge. Teal'c expresses his feelings that the Tritonin has made him weak.