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Daniel has uncovered evidence that a specific planet contains an Ancient repository of knowledge, similar to the one in season 2's "The Fifth Race", which downloaded itself into O'Neill's brain. He believes that this repository should contain the location of the Lost City they have been looking for. A Goa'uld probe was seen on the planet, so they must beat the Goa'uld to locating the repository. They hope to re-locate the repository back to Earth so they can study it and safely download its knowledge. The mission is risky, but given that the Asgard haven't been answering communications, their Jaffa and Tok'ra allies have abandoned them, and intelligence says Anubis is poised to conquer the system lords, General Hammond gives it a go.
Two other SG teams provide backup while SG-1 searches the ruins for the repository. When they locate it, everyone gives it a wide berth - rightfully so - but it's funny to watch. The Goa'uld arrive and attack immediately. O'Neill orders them to retreat, but Daniel and Carter say that the repository can't fall into Anubis's hands. So O'Neill sets up C-4 to destroy the repository, but they stop him from doing that, too. In desperation, O'Neill lets the repository download into him again. Then SG-1 retreats back to Earth, destroying the repository before they leave.
Because of O'Neill's previous experience with an Ancient repository, everyone knows what will happen to him: he'll gradually start speaking in Ancient, the Ancient knowledge will overwrite his brain, and eventually his body won't be able to handle it and he'll die. He's hoping that before he dies, he'll be able to access and communicate the pertinent information about the Lost City to the rest of SG-1. Although everyone is hoping a small miracle might happen, like the Asgard arriving to heal O'Neill, they all realize that he's essentially volunteered himself for a suicide mission. Since the first effects won't start for a few days, he takes that time to go home and put his affairs in order.
Meanwhile, the political events from last episode are shaking out in Washington. The president has decided to replace General Hammond as head of the SGC and to implement a full review of the program during a three month cessation of gate operations. He has chosen Dr. Elizabeth Weir as Hammond's replacement. We are told that she is well-known and well-respected in international politics and has negotiated a number of major international treaties. The president is clearly trying to put the best face on the SGC, in case it should go public, plus he is angling to manage the international politics of the stargate program that exist now. Dr. Weir is obviously qualified to handle the competing countries' interests in the stargate program, plus she should be able to negotiate with alien societies. And since she's not military personnel, the president can show the program is controlled by the civilian government.
Dr. Weir is initially overwhelmed at the existence of the stargate program, let along running it. She has always been anti-military and in favor of negotiation rather than force, so she does see the irony in being in command of essentially a military organization. However, she jumps into the job with the hope of being able to work for peace from the inside.
Vice President Kinsey is in the middle of all this, and firing on all engines. I get the impression that he won a victory in getting the president to agree to remove General Hammond and replace him with a civilian, but that he doesn't approve of the president's choice of Dr. Weir. Throughout the episode he puts pressure on Weir. He presents himself as her only ally, but then tries to effectively usurp her authority and intimidate her.
While O'Neill is relaxing at his house, the rest of SG-1 gradually stop by. First, Carter shows up. The tension between her and O'Neill is palpable. She clearly has a lot she wants to tell him, but just can't spit it out. This seems very realistic: few people are comfortable revealing deep feelings, and these two have been trained to be professional military and not let feelings interfere. Even if she doesn't have any more romantic feelings for him, they have been through a lot together and so he means a lot to her. She's also feeling guilty that she didn't download the repository into herself.
Daniel and Teal'c arrive, and for awhile the gathering feels almost like a funeral, even before O'Neill is dead. However, things must loosen up because we transition into a scene where O'Neill is comparing Mr. Burns (from The Simpsons) to the Goa'uld. General Hammond stops by (it's so strange to see him out of uniform - he looks shorter!) and tells them he's been relieved of command and that gate operations have been suspended. What does this mean for locating the Lost City, if O'Neill comes up with the location? No one knows.
After the weekend is over, SG-1 reports to the SGC for duty, although they apparently have nothing to do. Bra'tac arrives through the stargate (they are still answering "calls") to warn them that their Jaffa informants have told him that Anubis is gathering his forces and will arrive to attack Earth within three days. He stays to brief Dr. Weir and Kinsey.
This scene crackles with tension. The enmity between O'Neill and Kinsey is obvious. The rest of SG-1 also dislikes Kinsey, but not with the same palpable intensity. Dr. Weir is in the unenviable position of keeping the peace, but then again, she's a negotiator, so she should be good at it. O'Neill wants the SGC to start preparing for the arrival of Anubis (although I'm not sure what exactly they can do). Kinsey accuses SG-1 of manufacturing this threat to end the moratorium on stargate travel. Dr. Weir agrees that if O'Neill can come up with the location of the Lost City, she will consider authorizing a mission to it. During this scene, O'Neill begins slipping in Ancient words - clearly his transformation has begun.
When this meeting ends, Kinsey rips into Weir, saying that he wants all of SG-1 kicked out of the SGC, especially O'Neill. Weir very calmly tells him that she is in charge, and she'll make the decisions. She clearly has figured out Kinsey already! Kinsey makes a veiled threat and storms out.
Teal'c and Bra'tac leave for Chulak to try to scare up ships and warriors to help defend Earth. O'Neill says goodbye, just in case.
And that's it! This half of the two-parter is clearly mostly setup, but what setup. Just when possibly the worst threat ever is about the show up on Earth's doorstep, the only program capable of defending Earth is hamstrung by politics.
SG-1's mission at the beginning of the episode to the repository is a study of everyone's desire to sacrifice themselves for the team (and Earth). When it becomes clear that the only real choice is to download the repository, Daniel lunges for it, but O'Neill stops him. Carter later says she should have done it. I think O'Neill was right that he was the only logical choice: Daniel will need to translate the Ancient, Carter will need to deal with the weapons technology that will be discovered, and Teal'c may not even be able to use the repository.
In a way, O'Neill's sacrifice and possible death had been hanging over the episode from the beginning. We start the episode lingering over him as he shaves and works on a crossword puzzle. His phone conversation with Daniel is hilarious! But as we follow him, we get the sense that he's somewhat disconnected from events, as if he's already partly gone. He doesn't understand when Daniel gives him a puzzle answer. He delays his arrival at the SGC for a mission briefing so he can finish the puzzle (apparently with lots of wrong answers). He doesn't really seem to focus on the briefing, and seems almost resigned to the mission itself. But then he doesn't hesitate to doom himself using the repository; it's almost as if he knew it was coming.
The change of command of the SGC to Dr. Weir is an important development. I can see that it makes sense for the president politically, but I will miss General Hammond. Since the president wants to keep him around, hopefully we'll see him occasionally. Weir seemed a little wishy-washy at first, but when she finally stood up to Kinsey, you could see her nerve.
Bra'tac's reaction to Dr. Weir interesting - he immediately thought Hammond had died in battle. Apparently other options, like retirement, are not popular among the Jaffa. Although given the level of threat to Earth, I couldn't imagine Hammond retiring at this time. Bra'tac did not really greet Weir directly, but he seemed to take her seriously in the briefing. How will the Jaffa in general react to a woman being in charge of Earth's forces? Certainly some Jaffa women are very strong (such as Ishta from "Birthright"), but Jaffa women are generally taught to be subordinate to men.
The changing of power at the SGC has really left the defense of Earth in jeopardy. Dr. Weir cannot yet appreciate the danger of Anubis, or any Goa'uld. It's one thing to hear Daniel say that he will wipe out or enslave the entire Earth, but it's another thing to witness that happening - on another world, for example. Although, beyond giving O'Neill and SG-1 support in locating the Lost City, I don't know what could be done to prepare. Any conventional military forces would be useless. The available space-capable ships are extremely limited and so wouldn't be effective. We've even seen (I think) that nuclear weapons cannot penetrate Goa'uld shields. I suppose the best option would be to start preparing to evacuate key people to the alpha site, which is something we know is a contingency plan (which we saw in season 5's "Fail Safe").
I know that Kinsey is opposed to anything SG-1 suggests. However, given the number of threats that SG-1 has actually discovered an averted, you would think he would credit this. In fact, at the end of season 1, the final three episodes ("There But For the Grace of God","Politics", and "Within the Serpent's Grasp") were a sequence of Daniel finding out about a major threat to Earth, Kinsey dismissing it, and SG-1 disobeying orders to save Earth. This episode has nearly brought us full circle to that, and Kinsey hasn't learned a thing.
How will things fall out? When Anubis actually shows up, it will be a wake up call for many in the government. Hopefully Dr. Weir will rely on SG-1's experience and judgment, and not follow Kinsey's lead. We can only hope that O'Neill will gain enough of the Ancient knowledge in time for it to be useful.