Carter deduces that Thor had infected the ship with a virus while he was linked with it. That disabled the systems, causing Anubis and the crew to abandon ship. Then Thor ceased the self-destruct and sent the ship to Earth. The three Jaffas who are still aboard were just unlucky. The Jaffas go straight to the shield-generator room and kill Dr. Friesen, who disobeyed O'Neill's orders not to go there. The Jaffa proceed to the bridge and knock out Jacob/Selmak. They then disable the drive controls, which steers the vessel straight toward Earth. O'Neill calls Teal'c and orders him to extract the team. But it is the Jaffa who appear on the cargo ship instead. Teal'c takes out all three Jaffa, but during the battle the ring-transmission crystals are destroyed — stranding O'Neill, Carter and Jacob on a mothership about to crash into the North Pacific. Teal'c and Jonas return to Stargate Command, where Gen. Hammond immediately orders an undersea rescue via a Deep Submergence Rescue Vehicle (DSRV).

Under the sea, and with a weakened hull, the ship begins to take on water. Carter and O'Neill are trapped in the quickly flooding engineering level. Jacob/Selmak tries to override the system, but he fails. Suddenly, the doors open and Carter and O'Neill are free. Carter now surmises that the virus she thought Thor left behind was Thor himself. His mind took over the vessel, made the Jaffa abandon ship, stopped the self-destruct and brought himself to Earth in the mothership.

Teal'c and Jonas arrive in the DSRV and prepare to evacuate the survivors using the escape-pod tubes. Now O'Neill has a big decision to make: Thor's mind is the only thing halting the self-destruct. If SG-1 separates him from the ship's mainframe so that the Asgard can put his consciousness into a newly cloned body, the ship will explode. In the end, O'Neill decides that having the Supreme Commander of the Asgard fleet owe Earth a favor is better than claiming a barely salvageable mothership that would never fly again. Unfortunately, the tubes that Teal'c and Jonas used to enter the ship have flooded.

With Thor's mind removed from the computer drive, the self-destruct begins counting down. SG-1's only hope is to take a couple of Goa'uld gliders and pray they are seaworthy. But the force field, which keeps air inside the glider bay — or, in this case, keeps water out — after the hangar doors are opened has failed, and Jacob can't fix it. In the end it is Jonas who saves the day by diving down to a flooded deck, finding the relay panel, and bypassing the circuits that control the force field. The force field is enabled and SG-1 escapes via the gliders just before the ship explodes.

Original air date: June 21, 2002
Written by Joseph Mallozzi, Paul Mullie
Directed by Peter DeLuise

Cast
Richard Dean Anderson as Colonol Jack O'Neill
Amanda Tapping as Major Samantha Carter
Christopher Judge as Teal'c
Don S. Davis as Major General George Hammond
Teryl Rothery as Doctor Janet Fraiser
Corin Nemec (Jonas Quinn)
Carmen Argenziano (Jacob Carter/Sel'mac)
Colin Cunningham (Paul Davis)
John Shaw (Dr. Friesen)
Gary Jones (Walter Davis)

from scifi.com