While aboard their cargo ship, Maj. Samantha Carter and her father, Jacob/Selmak, scan a Goa'uld mothership in Earth's orbit, approaching them with shields and weapons down

About 100 kilometers from the vessel, Carter guesses this was the same ship that the system lord Anubis had used to kidnap Stargate Command's Asgard ally, Thor. SG-1 had saved Thor from Anubis, but Thor has remained in a coma since Anubis drained knowledge from his brain into the ship's computers. The ship is in perfect condition, power and life-support fully functioning, but abandoned with all its escape pods jettisoned

Col. O'Neill takes a team comprising Carter, Jacob, Dr. Friesen and Maj. Davis aboard the mothership to see if it can be salvaged, while Teal'c and Jonas Quinn stay behind

Jacob and Carter theorize that the ship belonged to Anubis himself. The self-destruct had been set but it is stuck in mid-countdown. A weird, electronic whispering emanates from the ship's intercom system. Carter and Davis go to the computer core to run a diagnostic and try to shut down the self-destruct. Jacob stays at the helm to do a systems check while Dr. Friesen and O'Neill go to see if the hyperdrive is intact

The engine checks out. Friesen wants to diagnose the shield generators, but O'Neill considers it more important to blow the fused-shut door to the computer core so that Carter and Davis can get through to find a way to disable the self-destruct

Unknown to SG-1, three Jaffa warriors who were trapped on the computer-core level escaped when Jacob opened the door to let in Carter. They did not register on the life-scanners because, through the Jaffa meditation known as Kelnoreem, they were able to hibernate and slow their heartbeats

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). Teal'c and Jonas join the effort

Aboard the Goa'uld mothership, Jacob raises the shields and sets inertial dampening to maximum, so that when the ship splashes down it will survive intact. 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. It was his garbled voice coming over the intercom the entire time. 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

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