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As the title of this episode suggests, there are many plot lines that are mostly separate, but intertwine in some places. First, Anubis calls Baal onto the carpet for his failure to conquer Dakara. He reveals that he does intend to use the Ancient weapon to wipe out all life in the galaxy, and is heading there. (It was very unclear about Anubis's whereabouts in "Reckoning, Part 2" - apparently he was not on Baal's ship.)
Next, the newly-created Jaffa nation, based on Dakara, is getting organized. They have organized a high council to rule them, and Teal'c and Bra'tac have both been asked to serve on it. Teal'c accepts, which may mean that he can no longer be so involved with the SGC.
The Jaffa currently control the Ancient weapon used in "Reckoning, Part 2", but don't really want to destroy it, despite O'Neill's and Jacob Carter's urgings. They realize that Anubis could still come to take the weapon. Although they cannot kill Anubis, they plan a preemptive strike against Anubis's forces with the goal of destroying all the Kull soldiers so Anubis will have no teeth.
Meanwhile, Carter and Pete Shanahan are working on wedding plans. While Jacob Carter is on Earth, Sam brings Pete to meet him. The meeting is spectacularly awkward - how realistic! Carter is becoming stressed out trying to fit in the wedding planning with her day job, which is giving her second thoughts. She also apparently still has some unresolved feelings for O'Neill; when she goes to his house (unannounced) to try to talk to him, she (and we) discover he's in a relationship with a CIA agent who has been working with the SGC. Even so, Carter calls off the wedding with Pete.
Then Jacob falls ill. Selmak has been weakening for some time because of his extremely old age. He wanted to choose to die and save Jacob (as Jolinar did for Carter in season 2's "In the Line of Duty"), but this was during the Replicator invasion and Jacob wouldn't allow it, because he thought they would need Selmak's knowledge. Selmak fell into a coma after the Ancient weapon was activated in "Reckoning, Part 2", and so now it's too late. Jacob will die along with Selmak.
O'Neill's relationship with the CIA woman is brief. After she sees him and Carter together, even in an innocent setting, she breaks up with him. Her parting advice to O'Neill is that he retire so that he and Carter can be together without breaking Air Force regulations. O'Neill seems to take this to heart, to some extent: he comforts Carter as her farther is dying.
Daniel is not dead. Intermixed with all the other "threads" in the episode, we follow his experiences in limbo: the waypoint where he is stopped temporarily while he decides whether he wants to ascend or die. Limbo is metaphorically represented as a diner, and Oma Desala is the waitress. Oma will not help him ascend if he is going to break the rules, and if he decides to take human form again (after ascending), he won't remember any useful information.
While in the diner, Daniel does find out about the history of Anubis and why he is a unique partially ascended being. Normally only a "pure of heart" being can ascend, and those are whom Oma helps. Anubis somehow learned about ascension and tricked Oma into helping him ascend, so that his powers would be magnified and he could wreak so much havoc on the galaxy. The other ascended beings prevent Anubis from doing anything horrible on a universal scale, but they do not involve themselves in single-galaxy affairs - and they keep Oma from interfering in these smaller atrocities as a way to punish her for her transgression in helping Anubis ascend. Anubis appears as one of the diner patrons and gleefully informs Daniel of his plans to re-take Dakara and destroy all life in the Milky Way galaxy.
Now the threads in the episode begin to tie together. The Jaffa attack on Anubis's domain is successful - but then they discover that all the defenses were automated, and that Anubis's forces are on the way to Dakara. Anubis begins to activate the Ancient weapon, and the stargates galaxy-wide are dialed. At the SGC, O'Neill orders the self-destruct on the possibility that the explosion might cause the wormhole to disconnect (which Carter says is very unlikely). Oma Desala realizes that while she cannot destroy Anubis, she can fight him and cause him to use all his strength in defense, effectively neutralizing him. When she does this, the Kull soldiers lose direction and the Jaffa on Dakara stop the weapon. The self-destruct at the SGC is somehow stopped with less than two seconds left.
Daniel is deposited in O'Neill's office while the others are meeting in the room outside. In a hilarious moment, O'Neill must choose between the US flag or the Air Force (?) flag to cover Daniel's nakedness. Daniel has all his memories, and reveals that Anubis is neutralized. Teal'c and Bra'tac inform everyone that the Jaffa have agreed that the Ancient weapon must be destroyed.
This episode was a great capstone to the events in "Reckoning, Part 2". First, it answer the question about what Anubis was going to do. I didn't care that much for the diner metaphor, but the backstory on Anubis and Oma was very interesting. Oma's compassion for "lower" beings, helping them ascend, has led her to make similar mistakes to those the SGC has made, albeit on a much larger scale. I find it nearly incomprehensible that the other ascended beings would fail to act to stop Anubis - why not just put him back into corporeal form? I can understand wanting to teach Oma a lesson, but it seems like they have gone a little far.
What is Oma and Anubis's fate? Will they battle as energy beings forever? Is there any chance of one somehow hurting or killing the other? Eternal combat to save billions of beings who are completely unaware that they are being saved is a poignant fate. It reminds me of a Star Trek original series episode where the galaxy is saved because the two Lazaruses (made of matter and antimatter) will fight each other forever.
Going from the extra-galactic to merely the galactic scale, I'm glad to see that the Jaffa nation has gained the wisdom to realize that neither they nor anyone else can be trusted with the Ancient weapon on Dakara. More practically, if the weapon still existed, the new Jaffa capital would be a target for any enemy power. However, we don't see the weapon actually being destroyed, so we can't count on its destruction yet.
A lot also happens personally for the characters, too. Teal'c and Bra'tac are made "blood kin" to all Jaffa. It's very satisfying to see them honored after their years of work toward Jaffa independence. It's also very appropriate to see them take places in the new ruling body. Will Teal'c really leave SG-1? As Bra'tac said, his goal in joining SG-1 has been realized, so it may be time for him to move on. I also liked that Bra'tac realized that keeping the Jaffa nation together now that their unifying element, fighting the Goa'uld, was gone would be very difficult.
Carter's life nearly falls apart in this episode. Jacob's death is sudden and very sad. Carter's decision to call off her wedding is also sad; but if she doesn't truly love Pete and want to have a life together, she shouldn't do it. She has consciously been trying to make some sense of her romantic relationships since season 7's "Grace", and it has obviously not been easy. When O'Neill comes to sit with her just before Jacob dies, he does seem to be reaching out to her and she responds. But just how far does he want to go? Will they actually begin a relationship?
Daniel is returned to the SGC - now he's died twice! Why did he get to keep his memories this time around? Who returned him, since Oma was otherwise occupied? It was convenient that he was returned to the SGC. How much of Daniel's Ancient knowledge that he uncovered with RepliCarter's help in "Reckoning, Part 2" does he remember?
In the grand scheme, the SGC and Earth are currently in a great position. Their main enemies, the Goa'uld and Anubis, are essentially gone. They are major players in galactic politics, with a good relationship with the new Jaffa nation, the Asgard, and various minor planets. They have a Ancient weapon on Antarctica that can defend Earth, although they currently don't have a power source. The SGC has nearly satisfied its reason for existence.