He took the submarine:
Originally Posted by Daniel_Jackson123
We have a rescue submarine docked with the ship.
Yeah…all right! Next mothership, we keep, okay?! Jonas, take Davis and Jacob back to the Sub, wait for us there.
Jack, we're at the sub. What's your status?
Jacob, I want you to get that sub to a minimum safe distance.
This is Jacob. We're a little seasick down here, but we're in one piece, too.
Jack, Sam, and Teal'c stayed behind to rescue Thor. When they were finished, they found that the path to the sub was now blocked:
This door should not be closed.
The corridor must have flooded.
Our exit is blocked. We need another way around.
Jack! All the other passageways into that section were already flooded. There is no other way around!
They then came up with the idea of trying the glider bay.
They recovered his body, but the fate of his mind was left up in the air. When they reached Thor, he explained that he was still connected to the ship's computer and pleaded with O'neill to leave him behind:
2) So Thor downloaded his consciousness into the ship? Maybe I'm misremembering, but didn't SG-1 save Thor from that ship earlier? Is it a mind-copy?
The link between myself and the Goa'uld ship has not been severed. They will be able to track our position. You must leave me behind.
Jack refused, and in the final scene this exchange happened:
What about Thor?
They managed to remove the device from his brain but it may have been too late. Apparently he's lapsed into a coma. If they knew more about how the device works they might be able to help him. They're studying it now towards that end. Unfortunately, it's unlike anything they've ever encountered before.
Basically, because the connection was still active, his brain fully downloaded into the Goa'uld computer after Jack made the decision to take Thor with him, and that's why he lapsed in a coma. This is confirmed in "Descent" when they realize that it was actually Thor controlling the ship and not a virus:
Sir, maybe what we've been calling a virus isn't a virus at all. Maybe it's Thor.
We got him off this ship months ago.
Not before Anubis was able to download his mind into the computer core. Now, if his consciousness remained intact, he would be an independent entity operating within the system.
He comes from an industrial society that is a few decades behind Earth (Carter described it as similar to Earth's 1940s) and has access to rich naquadria deposits that they were trying to exploit to give them an edge against rival countries. His speech and mannerisms are similar to Earth's because Stargate does not go very much out of its way to distinguish the speech patterns and mannerisms of humans from other planets. Some will have a more formal way of speaking (e.g. Teal'c), but for the most part they're distinguished as aliens by their saying they're aliens and occasionally mentioning that they don't get pop cultural references.
3) What's the story behind Jonas' world? He seems to act and talk like a kind of Earth person. I've been watching him since he appeared in the season 5 reruns (and on random eps before on SyFy), but forget some of what was said.
This is what he told Jacob:
4) How did Jonas know how to bring back the ship's power?
Cause I've gone over the schematics of these motherships a dozen times, and I'm a very quick study.
Thor never had a chance to explain his reasoning, but because the Goa'uld have interstellar (and not intergalactic) hyperdrives, piloting it to the Asgard homeworld wasn't an option. That leaves Earth as his best chance for getting help.
5) Was this ship really supposed to be a gift to SGC from Thor? I don't get why it was there and all that.
She was indeed an Ancient. I don't want to spoil anything from upcoming seasons for you, but basically there was a community of Ancients living there and that community left 5-10 million years ago to escape the plague. They left her behind because she was infected. She apparently succumbed to the elements and froze after being abandoned.
1) Why was that women frozen? Is she an Ancient? Never really understood where they came from, or her if she is.
Ayiana was able to heal everyone except for Jack, so the Tok'ra offered to heal him by temporarily implanting a symbiote in him.
2) What happened at the end of the ep? I can't remember.
Ayiana was infected with the plague and exposed everyone in the Antarctic base. She used her healing power to cure everyone save Jack. She did this as an act of self-sacrifice; healing all those people weakened her to the point where her power was no longer able to keep the virus at bay within her own body, so she died. Those she healed simply kept her body and Jack quarantined so they did not get reinfected.
3) And what did they do about the virus, and was it really coming from her, somehow?
After the second gate was found there, they set up a base so they could excavate the area around the gate and see if they could find anything else. When they discovered Ayiana four years later, Sg-1 and Dr. Fraiser were sent down there to analyze the find.
4) What was so special about going to the south pole? I know the second gate was found there, but...
You can read a summary here: https://www.gateworld.net/sg1/s6/nightwalkers/
1) Sorry, but what was the story behind this episode again? I can't remember now (it was late).