Okay. I think I need to explain this one to myself.
So our SG-1 went back in time and got stuck there because Sam was worried about changing history. But they couldn't just sit around and do nothing, so they decided to try and perpare the uprising against Ra. Only they got caught at it and our Sam, Jack and Teal'c were killed. Their actions changed the timeline so that Ra was defeated, but took the Stargate with him, and as such the SGC was never formed.
But the tape our team made was found, and the military got AUSam and AUDaniel to come on board and find the second Gate. AUKawalsky convinced AUJack to join the team to find AUTeal'c. AUDaniel gets snaked and dies, but the others make it back to Ancient Egypt -- the same Ancient Egypt where our SG-1 went.
They find our Daniel and figure out that the future was screwed up not because SG-1 came and brought the timeship, but because they interfered with the rebellion and Ra ended up taking the Stargate.
So... AUSam, AUJack, AUTeal'c, Daniel and Egyptian Guy now have to make sure that Ra is still defeated, but that he doesn't take the Stargate. Apparently they are successful (even though we don't see it) because - flash forward to 2005, during the end of Threads - the team looks pretty much like we left them. They have found the ZPM and the tape, which presumably is the same tape that AUSam and AUDaniel saw in Moebius 1, but everything that SG-1 says on the tape has come true. There's no discrepency. So they all go fishing just like they did at the end of Threads -- and realize that there is at least one discrepency: Jack's pond has fish. Close enough, they figure.
Oh yeah. And AUSam and AUJack so did it in the jumper.
So, ancient Egypt really saw 1 Daniel, 2 Sams, 2 Jacks and 2 Teal'c's. The first Sam, Jack and Teal'c were executed early on. The second Sam, Jack and Teal'c, as well as the first Daniel, helped the rebellion go off correctly and presumably lived out their lives in the past, and as such are long dead.
Things that jump out to me:
- Sam wouldn't let them retake the ship, but she would let them take part in the rebellion? That doesn't make any sense. In 1969 she wouldn't even encourage Michael
- Ra's theft of the Egypt gate meant that the SGC was never formed, at least not back in '97. I can accept that. It meant that Catherine never approached Daniel and he went on to live out his geeky life. I can accept that. But why would it mean that Sam never joined the Air Force? I know, I know... squishing a single butterfly in the past can change the world as we know it... old scifi concept. But come on, the two things seem totally unrelated.
- Jack's pond has fish. Is that just a way of making us wonder what else has changed for our SG-1? Or is it a sign? A shippy sign? I'm going with the latter :D
- Did I mention that they so did it in the jumper? In the words of Fry from Futurama, they did "the nasty in the pasty". I'm with coloneljack on this one. Everyone in the present day who has the Ancient gene is a descendant of AUSam and AUJack's babies. Which makes Jack his own ancestor, which is cool. Makes Sam his ancestor too, which is kind of weird.
pixiesio also has some interesting thoughts on this.