On an alien planet, SG-1 discovers an inactive android is the only survivor of the destruction of her civilization. They bring her back to the SGC for study and manage to reactivate her. Things take a turn for the worse when she "makes" a replicator bug for Daniel.

Teal'c is having strange nightmares featuring Apophis in which he is human and a firefighter with the rest of his team alongside him.

On a shakedown cruise of the Prometheus, the ship's hyperdrive regulator becomes irreparably damaged. A nearby planet was listed on the cartouche of addresses found on Abydos and thus may have a stargate. After a short jump towards the planet, the Naquadria reactor overloads and must be jettisoned. After the reactor explodes above the planet causing damage, the fate of SG-1 and the crew of the Prometheus is in the hands of a once Goa'uld-controlled world that they're off to a rough start with.

On a routine mission, SG-1 encounters a civilization desperate to be freed from the clutches of a Goa'uld. While on the planet, Jonas falls ill and is suspended from active duty. His mysterious illness is diagnosed as a brain tumor but gives him the unbelievable ability to glimpse the future, a future where O'Neill and SG-1 are walking into a trap!

When an SG geological exploration mission runs into deadly conflict with an indigenous Unas clan, Daniel gets Chaka to help seek an accord with it.

Bra'tac and Teal'c encounter a heavily armed enemy with shielding protecting him from Goa'uld weaponry who took out two Goa'uld personal guards. They barely manage to defeat him and bring him back to SGC for study, but this new threat poses a greater problem for the Tau'ri.

General O'Neill is still in the early days of commanding the SGC and faces a major problem when newly arrived Russian Col. Alexi Vaselov collapses in his quarters. Dr. Brightman's belief that Vaselof may be contagious seems correct when Daniel, who was with the Russian when he collapsed, apparently goes mad and tries to leave the base through the gate. O'Neill locks down the SGC but the problem isn't contagion: the essence of Anubis is alive and well and seeking a new host.

Dr. Lee is adapting a virtual reality chair for use as a training device. Teal'c thinks its current scenario is all too easy and agrees to work with them to make it more realistic. He enters the game scenario and is quickly "killed" at which point the chair shocks him. Lee says it must be part of its basic construct. As the scenario resets - it's an invasion of SGC by Goa'uld - Teal'c is repeatedly killed and shocked putting him in danger. The computer program is set up to learn after each scenario and the challenge for Teal'c increases at every turn. Daniel volunteers to enter the game as well to see if together they can find a way out.

After a long absence, Jacob Carter returns to the SGC to tell Jack that the galaxy is under threat of takeover by the Replicators. The Goa'uld are under attack from the Replicators and are quickly being eliminated. Ba'al's armies are being destroyed and he arrives at SGC to suggest they work together to defeat their common enemy. Carter's doppelganger, RepliCarter, is leading the attack and she has kidnapped Daniel Jackson in the hope of learning of any weapons the Ancients may have created that could defeat them. Jackson gets help from an unexpected source - the Ancient, Oma Desala - or so he thinks.

Vala leads SG-1 to a planet which the Priors have visited with a plan to keep them from worshiping the Ori. Once there she reveals that the symbiote that once held her ruled over this planet. She feels that keeping them in allegiance to her will hinder the spread of Origin to this world.