SG-1 heads for the Goa'uld mothership that belonged to Anubis when he kidnapped Thor and Downloaded his mind onto and is now abandoned. This mission was that alien eager-beaver Jonas Quinn's initial one with SG-1, and he had that first-time-at-Disneyland smile on his face. He'd never been in space before and waxed poetic about how thrilling it was. Teal'c agreed. So did I. Space travel is thrilling — until something goes horribly wrong. O'Neil has Major Carter, Major Davis, Dr. Freisen and himself go to the ship, Jonas is ordered to stay aboard the Cargo ship with Teal'c but he doesn't want to, he thinks he should go because he has studied every Report of SG-1 but it was because O'Neil just said that he couldn't come. Jacob has them ring aboard to check things out rather than to fly into the cargo bay to determine if the ship can be salvaged.
When aboard they descover that the ship was indeed that which captured Thor a few months back. They also find that the ship was in Self-Destruct mode but the countdown was paused but it doesn't make sense because the countdown should have been reset not paused; there was some weird electronic whispering that was emanating from the ship's intercom system. O'Neil has Major Carter and Major Davis go to the Computer core when they find out that the door was locked and life support was shut down, Jacob opens it and regains life support. O'Neil and Dr. Freisen take a look at the engines an hyperdrive where intact. They checked out. Dr. Freisen wanted to look at the sheild generators because they must have been superior to others but because it wasn't priority O'Neil doesn't let him. Meanwhile Carter & Davis find a door that was hit by several Staff Blasts and it can't be opened even by Jacob because the circuts where fused. Carter calls O'Neil so he tells Freisen to head back to the helm while Jack blows down the door into the computer core to do a diagnostic to shut down the self-Destruct. What we didn't know was that there where 3 Ninja Jaffa warriors were trapped on the computer-core level and escaped when Jacob opened the door to let Carter in. Jacob later told Jack that they didn't show up on the life scanners because they were able to hibernate and slow their heartbeats by putting themselves into "kelnoreem." Who trapped them in there was still a mystery. Carter supposed that Thor had infected the ship with a virus while he was linked with it. That screwed up the systems, causing Anubis and crew to abandon ship, then ceased the self-destruct and sent the ship to Earth. The three Jaffas were just unlucky. But now the Jaffas were out and they went straight to the shield-generator room where Dr. Friesen had gone even though Jack ordered him not to. Dr. Friesen was dead. O'Neil found his body in the room. Then the Jaffa went up to the bridge and shot Jacob. They also disabled the drive controls and so the ship started towards Earth's atmosphere fast. Jack called Teal'c and told him to ring them out. But when he activated the transport rings, the Jaffas appeared on our cargo ship. Teal'c took out all three in seconds, but during the battle, the ring-transmission crystals had been destroyed. We were stuck on the mothership about to crash into the North Pacific. Meanwhile Teal'c & Jonas headed back to the SGC. Hammond ordered a rescue via a Deep Submergence Rescue Vehicle. Teal'c and Jonas joined the effort. Jacob had raised the shields and set inertial dampening to maximum so when the ship splashed down, the ship would survive in one piece. But they were under the sea. And to make matters worse, the impact weakened the hull and the ship's lower levels were flooding, including the engineering level where Carter and Jack were. Suddenly, the security protocols locked the door on them and they were going to drown. Jacob tried to override the system, but no luck. Just when Jack was experiencing major shrinkage, not to mention lack of air, the doors opened and they were free. Carter now surmised that the virus she thought Thor left behind was Thor himself. It was his garbled voice coming over the intercom all this time. His mind took over the vessel, made the Jaffa abandon ship, stopped the self-destruct and sent Earth the mothership. Way to go, Thor! Teal'c and Jonas arrived in the DSRV and were ready to get them out using the escapepod tubes, but they had a big decision to make. Thor's mind was the only thing halting the self-destruct. If we separated him from the ship's mainframe so the Asgard could put his consciousness into a newly cloned body, the ship would explode. In the end, Jack decided that having the Supreme Commander of the Asgard fleet owe me one was better than a mothership that would never fly again. But the next mothership we keep. But they weren't out of the water yet. The tubes Teal'c and Jonas used to get in through were now flooded. And now that Thor was removed the computer drive containing Thor's mind, the self-destruct was counting down. Their only hope was to take a couple of death gliders and hope they would fly underwater even though they aren't built to operate Underwater. But now there was another problem. The force field that prevents space or in this case, water from flooding the Glider bay after the hanger doors were opened was not operating (The shield is used instead of having to pressurize the compartment everytime). And Jacob couldn't fix it.
Well, Jonas, finally proved his mettle by diving into a flooded deck to a relay panel and bypassing the circuits controlling the force field. It was on! Jonas joined them and they all got out of there, just before the ship blew to pieces