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Dr. Daniel Jackson makes an amazing discovery while translating the Ancient writing on the colonnade that SG-2 discovered on planet P3X-439. The writing talks about a library of knowledge and Daniel suspects it contains a repository — the same type of device that once downloaded the Ancients' knowledge into Col. O'Neill's brain and would have cost O'Neill his life had not the Asgard intervened and removed the alien data from his mind.

However, SG-2 spots a Goa'uld reconnaissance drone while on the planet, which means that system lord Anubis is also aware of the repository's existence. SG-1 must get to it first, so that they can, once and for all, learn the location of the Lost City of the Ancients and use that race's advanced technology to save the galaxy from Goa'uld oppression. Should this knowledge fall into Anubis' hands, nothing will be able to stop him. This time, SG-1's plan is to remove the repository rather than downloading it into a human, and then to bring it back to Earth and find a safe way to retrieve the data. The Asgard and other alien allies are not responding, so Stargate Command is on its own.

SG-1, SG-2 and SG-3 are dispatched to P3X-439, where Daniel and Maj. Carter try to remove the repository from the monument — with no luck. Suddenly, a full-scale Goa'uld attack rocks the monument, as Alkesh fighters carpet-bomb the area. There is no choice: Someone must download the Ancient knowledge into his or her brain. O'Neill assesses that Carter is too valuable, and that Daniel will be needed to translate the Ancient language that whoever goes through with this will be speaking when their consciousness is taken over and replaced by that of the Ancients — resulting in neural overload and death. So he does it again: O'Neill steps up to the repository, where the face-hugging arms come out, grab O'Neill's head and pump Ancient knowledge directly into his brain.

The teams return to Stargate Command, where they must face the inevitable: O'Neill's human consciousness will soon be obliterated and he will begin speaking in Ancient. Not long after that, his human physiology will no longer be able to handle the strain and he will die.

Meanwhile, in Washington, newly inaugurated President Hayes has found a replacement for Gen. Hammond, in an attempt to put a friendly face on the Stargate Project when it goes public. She is Dr. Elizabeth Weir, a multilingual political negotiator who will be able to confer with leaders of other countries, who no doubt will want shared control of the stargate.

Indeed, there's already someone within the administration itself who wants control of the stargate — Vice-President Kinsey, who has pressured the president into this bold move. Kinsey informs Weir in no uncertain terms that he is best person to have on her side when she takes over Stargate Command — and the last person she'd want to cross.

President Hayes, completely aware of Kinsey's history with Hammond, informs the general that he does not want him to retire. He knows full well that Hammond's experience will remain invaluable in the near future — but politics is politics. All offworld teams are recalled and the stargate is shut down for a three-month review process.

No one at Stargate Command is happy about that, or about Dr. Weir taking command. For her part, Weir doesn't intend to allow Kinsey to use her as a puppet to control the stargate. She is also aware of O'Neill's impending death and intends to deal with it. Kinsey wants O'Neill and the rest of SG-1 gone, but O'Neill's knowledge of the Lost City is crucial to winning the war against the Goa'uld.

The Goa'uld, meanwhile, are now an immediate threat to Earth: Teal'c's mentor, Bra'tac, arrives through the stargate with the dire news that Anubis knows Earth has the repository of Ancient knowledge, and he is about to attack. In three days, he and his army of Kull Warrior supersoldier drones will arrive.

Kinsey thinks this is all a ruse to keep the program running and SG-1 in place. But Weir knows better. — and because the knowledge in O'Neill's head is the only chance of saving Earth … well, Kinsey's private agenda be damned. She's in charge of Stargate Command now, not him. She believes that the threat to Earth is real and that America owes Col. O'Neill the chance to make what might be his ultimate sacrifice. Judging from the Ancient word that issues from his lips, the time for that sacrifice is coming soon.

Bra'tac returns home to Chulak. Teal'c goes with him, in the hope of procuring warriors and ships to protect Earth. O'Neill is about to give Teal'c the "if I don't see you again speech." But Teal'c is certain they will. The rest of SG-1 hopes he's right.