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At the end of the first part, we had many plot threads going on: on Earth, a Goa'uld ship was approaching to "test" Earth's defenses while the three Goa'uld mediators were held by the SGC; in Antarctica, O'Neill was still in stasis; in the Asgard galaxy, the Asgard had just destroyed the Replicator ship, presumably killing Carter as well.
First, I'll discuss the plot on Earth. Because of the Goa'uld threat, Dr. Weir ordered Yu, Camulus, and Amaterasu placed in the brig. Oddly, no one at the SGC really tries to interrogate them or otherwise get any information from them. Fortunately, Earth's secret (that they might not be able to use the Ancient defenses again) is safe, because Baal destroys the Goa'uld ship before it gets to Earth. He has solidified his hold over the other Goa'uld. Since the immediate threat is over, the SGC releases the three Goa'uld. However, Camulus asks for (and gets) asylum on Earth; he claims that his forces have already been assimilated by Baal and so he has nothing left to return to and would face a life of serving another Goa'uld. I realize the SGC is hoping to gain useful information from Camulus, but I have to think that he has another motivation here - after the Goa'uld's attitudes toward human food and hospitality, I can't imagine he'd want to stay there indefinitely.
Now, to the Asgard. While the Asgard did destroy the main Replicator ship, some of the Replicator blocks in the shrapnel of the explosion have fallen to the surface of the new Asgard homeworld, and the Replicators are rapidly adapting and destroying the Asgard civilization. (Replicator survival through re-entry of an atmosphere was established way back in season 4's "Small Victories".) Thor decides that the Asgard's only hope is to access the Ancient knowledge in O'Neill's mind in order to find some type of weapon to use against the Replicators. He quickly takes his ship (with Teal'c) back to Earth, and picks up Daniel and O'Neill (still in stasis).
Thor connects O'Neill's mind to his computer so that O'Neill can utilize the Ancient knowledge without the risk of removing him from stasis. This leads to a scene that reminds me very much of the classic Star Trek episode "Spock's Brain": instead of Spock, O'Neill's voice comes from the computer. How is Thor's computer able to perfectly simulate O'Neill's voice? Spock commented on how he "felt" he was breathing and his heart was beating as his automatic systems ran life support - O'Neill in typical fashion gets some thrills out of turning the lights on and off. But, unlike the Star Trek episode, O'Neill's body is not automated; instead he appears as a hologram. He builds some kind of device, but before he can finish it and explain what it does, his failing body requires that he be removed from stasis. Once his body is revived, he cannot remember what the device is or how it works, and Thor can't figure it out. Wow!
Thor returns them to the new Asgard homeworld. In order to figure out what O'Neill's device does, he brings aboard a mostly-dead human form replicator from the Replicator ship debris. He is certain that if it does recover, he can either contain it or beam it into space. Talk about hubris! Of course, the human form Replicator escapes from confinement, but O'Neill's instincts take over, and he uses the device to cause the Replicator to disassemble into its most basic, inert blocks. Upon seeing the weapon in action, Thor is able to modify his ship to produce the same effect on a planet-wide scale, once it fully charges.
Meanwhile, we learn that Carter is not dead after all. She awakens on a farm where she apparently lives with Pete Shanahan (from season 7's "Chimera") after having resigned from the SGC. She instinctively feels that this life is wrong, but Pete almost convinces her it's right. She eventually realizes that Fifth is playing out this scenario for her for some reason, and she demands that he show himself. "Pete" dissolves into Fifth, who reveals that he loves Carter. Obviously he does not have the human experience or maturity to really understand what love is, and just as obviously he has a psychopathic personality. Carter is stuck trying to deny his feelings while not angering him so much that he kills her out of hand. She finally throws caution aside and tells him that no matter what she will never reciprocate his feelings and cooperate with him.
On Thor's ship, Carter's lifesign is detected on the planet's surface, and the rest of SG-1 mount a rescue. They are quickly surrounded by the primitive, bug-like Replicators, but are holding their own using O'Neill's new weapon. Fifth cannot stand the destruction of his minions and threatens to kill Carter if they don't stop; they comply for the moment. However, Fifth has clearly figured out Thor's plan and is calling the Replicators to evacuate the planet. Thor's super-weapon isn't quite ready yet, so he calls on SG-1 to slow the Replicators down. They are apparently prepared to sacrifice Carter's life for this and again attack the Replicators.
Unfortunately, they are not successful in preventing Fifth and some of his minion Replicators from leaving the planet. The rest are destroyed when Thor activates the weapon. At least some of the Asgard civilization is saved. Fifth abandons Carter, so the whole of SG-1 is reunited.
Upon return to Earth, we find that Dr. Weir has been transferred to command of the Antarctic project of deciphering the Ancient base and coordinating the international effort. O'Neill has been promoted to brigadier general and is given command of the SGC. His first act is to promote Carter to lieutenant colonel.
The eerie tag of the episode is when we see that Fifth has created a Replicator version of Carter - presumably one that will be more responsive to his feelings. He tells her that they will be unstoppable.
Wow, there's a lot that happens in this episode. I have to say that sometimes I find the Asgard just a little annoying. Obviously they have done a lot for Earth, but their arrogance, while understated, is amazing. First, Thor puts off healing O'Neill, but then when the Asgard need his knowledge - off to Earth we go! And then the whole beaming-people-up-without-asking thing is pretty annoying. Also, you'd think with how many times the Asgard have devised a plan to destroy the Replicators only to have it fail, they wouldn't be quite so confident in the next plan. Putting all their eggs in one basket on their new homeworld was not the smartest plan, either. Although I suppose that they have not met anyone who could challenge them in so long that they aren't used to it.
At least they know how to honor SG-1: naming ships after them. At least the Daniel Jackson wasn't destroyed, like the O'Neill was. The confusion between O'Neill and Daniel about the ship's name was a funny bit...also O'Neill's repeated questions to Teal'c about his new hair, which conveniently keep going unanswered.
This latest evolution of the Replicators is unsettling. The original (bug-like) Replicators were disturbing and frightening because of their huge numbers, adaptability, implacable nature, and faceless nature. The human form Replicators that developed in season 6's "Unnatural Selection" took away their alienness and made them seem familiar, which also made them less scary. However, Fifth's ascension to power and his psychopathic nature, combined with a Replicator's abilities, renews their threat. What will Fifth's next move be, once he has let his minions multiply? Is he still motivated solely by the Replicator goal of finding more advanced technology? Or will he be more motivated by revenge - against the Asgard, or against Carter?
Fifth's attempt to delude Carter into a illusory life with him was another aspect of the episode that is a stock Star Trek plot. And true to Star Trek tradition, Carter rejects such an illusion, even if it is very appealing and pleasant. Incidentally, does this mean that Pete Shanahan is still in Carter's life?
I was a little disturbed by how quickly O'Neill and the others essentially forfeited Carter's life and went back to killing Replicator's after Fifth's ultimatum. I realize that stopping the Replicators was much more important, but they didn't even discuss it. Earlier in the episode, Daniel had protested possibly killing O'Neill in order to access the Ancient knowledge, but now he doesn't protest risking Carter's life? They had no way of knowing about Fifth's obsession with Carter and that he would likely not kill her because of that. After the Replicators are gone and Carter is found, no mention of it is made.
The end of the episode is a nice wrap-up for the beginning of the season. It does actually make sense for Dr. Weir to head up the project with the Ancient outpost (which we know will lead into the series Stargate Atlantis). It also makes sense that the only military person all the countries would accept commanding the SGC would be O'Neill, who has personally saved the planet many times and is infamous for not being politically motivated. The scene where O'Neill discusses the pros and cons of his promotion with SG-1 is hilarious. It also obviously sets the stage for O'Neill to make changes at the SGC and to be more "hands on" in his command than Hammond was. What will happen with SG-1? Will he be replaced?
We are left with a "new order" in the Stargate universe in several ways. Obviously, the SGC has a new commander. Galactic politics have been completely upset. The Goa'uld now consider Earth to be a major player because of their Ancient weapons. Baal is now the dominant power since Anubis was defeated. The Asgard have a weapon to use against the Replicators, who are still at large. The leader of the Replicators, Fifth, may have a grudge and also has created a copy of Carter.