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The beginning of the episode focuses on a negotiation between Yu (representing the unconquered system lords) and a minor Goa'uld acting on behalf of Baal. Baal is offering to let the remaining system lords continue to rule their empires, but they must themselves be ruled by Baal. Not surprisingly, Yu doesn't look favorably on this idea. However, events take an abrupt turn in a different direction when a captured "Carter" is brought in. We quickly learn that this is RepliCarter (the human-form Replicator that was copied from Carter), and she rapidly kills Yu and the other Goa'uld and Jaffa there by transforming an arm into a sword, a la Terminator 2. And so ends the system lord opposition to Baal.
Meanwhile, SG-1 is acting as "observers" of actions by Teal'c, Bra'tac and the Jaffa rebellion. The time has come for the coordinated attack Teal'c spoke of in "Sacrifices": simultaneous Jaffa uprisings have been organized in key locations of Goa'uld power. They couldn't have picked a worse time! The new Replicator campaign against the Goa'uld, especially Baal, has destroyed the organization of the attack. The spaceship with Teal'c, Bra'tac, and SG-1 is attacked by a Goa'uld ship that has been taken over by Replicators: the Replicators beam Daniel away, much as they did Carter in "New Order, Part 2". The rest are forced to abandon their ship to the Replicators and use the stargate on the planet they are orbiting to travel back to the SGC.
In the meantime, Jacob Carter arrives at the SGC - the first time we have seen him since last season's "Death Knell" when he left to mend some fences with the Tok'ra high council. He has not been totally successful in that respect, but his concern about the Goa'uld/Replicator war is too great to stay away. He stole a Tok'ra device that monitors the locations of Goa'uld ships and brings it to the SGC so they can track the war. It is clear that the Goa'uld are losing rapidly.
Now the SGC is faced with the possibility of the Replicators wiping out the Goa'uld and taking over the galaxy, and Teal'c and Bra'tac are faced with the possibility of the Jaffa rebellion fading away to nothing. When Teal'c and Bra'tac assess the new situation, they learn that many of the rebel Jaffa are repledging their allegiance to their Goa'uld masters: either in genuine repentance to their "gods" or because they believe that only the power of the Goa'uld can defeat the Replicators.
O'Neill sends Carter to work with Thor to see if the anti-Replicator weapon can be altered to counteract the immunity that RepliCarter programmed in "Gemini". Carter suspects that RepliCarter kidnapped Daniel in order to squeeze Ancient knowledge from his mind from when he was ascended. Carter travels to Thor's ship, where they perform some experiments.
In the meantime, Teal'c and Bra'tac devise a daring plan to reignite the Jaffa rebellion: they will conquer the world of Dakara, currently under Baal's rule. It is the most important world to Jaffa, because it is the location of many ancient rituals and events between the Goa'uld and Jaffa. They believe that if they conquer Dakara, most Jaffa will renounce the Goa'uld. Their reasoning about why this campaign would be successful now is that the usual forces Baal would have guarding Dakara would be out fighting the Replicators.
O'Neill and Jacob argue about the best way to handle the Goa'uld/Replicator war. Jacob wants to give Baal "hints" on how to fight the war so that it will be prolonged (presumably thus delaying assaults on Earth and other worlds). O'Neill is worried that in that case, Baal would fall back to Dakara, ruining the Jaffa rebellions chances. In fact, Baal transmits an image to the SGC to ask for help fighting the Replicators. O'Neill demurs, and does not pass on Jacob's advice.
The rebel Jaffa take over Dakara easily - without a fight apparently, since we didn't see one. However, Bra'tac is wise enough to realize that the true fight will be to keep control of Dakara once Baal finds out they are there. In the biggest twist of the episode, we learn that Baal is actually following Anubis's orders. Somehow Anubis survived being trapped on the ice world at the end of "Lockdown" and has apparently been transferring from human host to human host as they sicken and die. Anubis wanted the rebels to take over Dakara; once they did, he orders Baal to re-take the world and wipe out the rebellion.
Carter and Thor believe they have a successful modification to the weapon, and track down a solitary Replicator ship to test it. It apparently works, but when a second Replicator ship arrives, they adapt to the weapon and it is ineffective. Thor's ship is boarded; he returns Carter to Earth and then intends to get his ship as far away from Earth as possible before the Replicators take over completely.
During all of this, RepliCarter is beginning her interrogation of Daniel. She uses the Replicator mindprobe technique to dig through his memories. She believes his subconscious retains the knowledge he had when he was ascended. During the probe, she creates visions to trick and confuse Daniel (similar to what Fifth did to Carter in "New Order, Part 2"; she makes an image of Oma Desala to encourage Daniel to think about his ascended experiences. She finally gets the information she wants: the location of the only weapon in the Milky Way that could destroy her. Of course, it is located on Dakara.
Baal is not comfortable with Anubis's intentions and contacts the SGC again. He tells them of the weapon on Dakara, and reveals that not only could it destroy the Replicators (a good thing for everyone) but could also be used to destroy all life in the galaxy (a bad thing for everyone). He asks that the SGC and the rebel Jaffa destroy the weapon before his forces can reclaim it: otherwise Anubis might use it on everyone. O'Neill is not thrilled to hear that Anubis is still alive, and the episode ends.
This episode has a lot going on! However, all the different threads of the plot are pretty logical and hang together well. We knew that RepliCarter and the Replicators were bent on galactic domination, and it was just a matter of time before they got started. The Jaffa rebellion has the bad luck to start their own campaign at the same time. I think that the rebel Jaffa being unnerved enough by the bizarre Replicators and thus returning to the Goa'uld rings very true.
I like seeing the SGC becoming a hub between different factions again. After season 7's "Death Knell" when the SGC-Tok'ra-rebel Jaffa alliance broke up, I believe the efforts against the Goa'uld were seriously weakened. Since that time, the rebel Jaffa have been keeping in contact with the SGC to some extent, since Teal'c is a major leader in the rebellion. But they have been careful to keep their command structure separate so the SGC could not tell them what to do: SG-1 being "observers" at the beginning of the episode was a good example of this. At least the lines of communication are open!
Communication with the Tok'ra since then has been much scarcer, to the extent that Teal'c believed it was possible that the Tok'ra had begun using symbiote poison on the Goa'uld (in "Endgame"). Clearly, the Tok'ra haven't decided to ease relations with the SGC - Jacob Carter took matters into his own hands. I'm not completely sure why Jacob came to the SGC. It was a good way to notify the SGC of the Replicator/Goa'uld war, but what else did he hope to accomplish? Does he believe the Tok'ra will sit back and let the Replicators take over? I suppose he knows that the SGC and the Asgard have made the only (previously) functional anti-Replicator weapon, but he doesn't even mention that. However, events happen so quickly, that possibly his initial plans became irrelevant. O'Neill and Jacob have a lot of great dialog. I enjoy watching O'Neill spouting his usual witticisms when things aren't too urgent, and then quickly asserting his command decisions when he refused to tell Baal Jacob's advice.
The return of Anubis is not entirely unexpected, but is still a welcome wrench thrown into the works. How long has Anubis been directing Baal? What power does Anubis have to compel Baal's obedience, anyway? When Anubis was stranded on the ice world, he seemed pretty vulnerable. Presumably one of Baal's ships picked him up for some reason - how did he rise back to power? I can think of a few possibilities. First, once he returned back to his old domains, he could have activated some kind of override to return the Kull soldiers to his control (not Baal's), which would immediately give him dominance. Second, he may have threatened to take over Baal's body, which would cause it to die (along with the host, I would imagine). Third, he may have promised Baal extensive knowledge from his time as an ascended being and thus power. I'm thinking the first is most likely, because I think Baal is smart enough to either work around or not fall for the last two.
How did Anubis know that the rebel Jaffa would take over Dakara? He acted as though that was his intention, but the Jaffa themselves considered the plan to be incredibly audacious. Possibly Anubis was just putting a good face on events and then taking advantage of them. Anubis clearly knows about the weapon on Dakara, since Baal knows about it. Why hasn't Anubis used it already, especially given the Replicator threat? Does he really want to wipe out all life in the galaxy? If he did, who would grovel for him? It seems like absolute power wouldn't be any fun if you didn't have anyone to exert it over.
The plot involving Thor, Carter, and the anti-Replicator weapon was a bit of a red herring, since it didn't yield any results. However, it was a logical course of action for the characters to take, and not every plan works.
I was a little sad to see Yu killed off, since he was such a wily warrior, but I also like seeing actual changes in the political setting of the series. I have to wonder, though, was his comment about Anubis still being alive in "New Order, Part 1" really a slip of the tongue, or did he somehow know something?
This first part of the two-part episode has nicely set up events for everyone to converge on Dakara in the next part. RepliCarter wants to destroy the weapon. The SGC wants to use it to destroy the Replicators. Anubis wants to use it to destroy everything. The rebel Jaffa are sitting on a land mine, and they have no idea - yet! This episode was a pleasure to watch since it drew on so many of the different on-going plots in the series and brought back a number of recurring characters.