Setup for Atlantis (and the last few eps of the last SG1 season):
On some planet, the team runs into another one of the head-sucker information machines. The last time they’d run into one it grabbed O’Neill, crammed the knowledge of the Ancients into his brain, and eventually led to first contact with the Asgard (to remove said knowledge before it overloaded O’Neill’s brain and killed him). A few moments after finding this new one, the team is under attack by Go’auld. Rather than let it fall into enemy hands, O’Neill sticks his head in it again then destroys it before escaping through the gate.
Problem: The Asgard aren’t coming to the rescue this time. They’re spread incredibly thin fighting the Replicators, and nobody’s answering the SGC’s calls. While O’Neill can still communicate in English Daniel grills him on possible locations of the Lost City.
Another problem: Anubis is heading for Earth with his super ultra mega mothership, and with his fallen Ascended powers and super soldiers is a major threat not just to Earth but to everything in the galaxy.
O’Neill loses the capability of speech, but dials an unknown address into the gate. Following him, the team find what appears to be a deserted Ancient outpost. O’Neill pulls something (the first appearance of the Z(ed)PM, seen in Atlantis and some of the recent eps of SG1) out of the floor and messes around with some sort of map. It pinpoints the location of the Lost City: Earth!
Everybody heads back to Earth. There’s no Lost City, but O’Neill uncovers another outpost in Antarctica. He pulls something out of the floor and replaces it with the one he took from the first outpost, then sits in a glowy chair. This activates the Ancient Defense Mechanism, which blows seventeen kinds of crap out of Anubis (see: the drone that went nuts in the opening moments of the pilot Atlantis episode). O’Neill unplugs himself from the chair and puts himself in suspended animation before the Ancient knowledge makes his head a splode.
All these fireworks don’t go unnoticed by the international community, which is why the Stargate program had to be revealed to all these other governments. They’re naturally miffed and demand to be part of the 'Gate program, and they can’t all be ignored like the Russians.
Carter and T’ealc make their way to the last known location of the Replicators (the ‘homeworld’ which had been trapped in a time-dilation device to imprision them for a few thousand years until something better could be figured out to deal with them) to look for the Asgard in order to save O’Neill. Sure enough, Thor’s there but didn’t pick up all the SGC distress calls because the time-dilation was messing with his communications. The Replicators have mucked around with the time doohicky and it’s a) failed to work and b) made them even more powerful. Thor beams O’Neill aboard and hooks him up to his ship’s computer for a moment in order to talk with him without killing him. O’Neill in his hyperintelligent state whips up a funky raygun prototype, but Thor has to remove the Ancient knowledge from O’Neill’s brain before he can explain what it is. Five (the humanoid Replicator with feelings) feels betrayed by Carter (because he was) and captures her while the Reps attack Thor’s ship. O’Neill’s funky ray turns out to be a Replicator blaster (it reduces them to their component Lego blocks and makes those inert so they can’t combine again), and he rescues Sam from Five’s clutches. Thor adapts O’Neill’s funky ray into a shipboard cannon, and cleanses an Asgard colony of Replicators. Five escapes and builds a naked Carter clone, promising sweet sweet revenge.
While all this was going on, back at the SGC Hammond was replaced by Weir (a civilian! Egad!). It turns out Hammond was promoted to the Pentagon, and Weir’s taking his place. She and Daniel completely fail to create a treaty with some of the remaining Go’auld System Lords concerning the power vacuum left by Anubis’s death. Lord Yu is in particular tricky; he’s refused to change hosts for so long that he’s going senile, but nobody dares mention it.
Weir also fails to inspire any confidence as a leader in the SGC. She’s phased out in the last episode of last season; O’Neill’s promoted to Brigadier General. Weir gets to lead the Atlantis team; O’Neill takes over the SGC operations. The first thing O’Neill does is promote Carter to Colonel and make her team leader of SG1.
Good news: The System Lords all fear Earth because we took out Anubis. Bad news: we don’t have the juice to fire the defenses again, so it’s a huge bluff.
Atlantis was on Earth, but now it’s not. The Ancients packed up and left thousands of years ago, but they left a forwarding address. This address is in a far-off galaxy; so far that the power requirements of Gate travel mean that they’ll only get one shot to open a link there.
T’ealc grows hair. Nobody explains why it’s a different color from the chin thing he had a few years ago.
