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SG-1 is on a newly-dominated Ori world, covertly observing Adria giving a speech to her new followers. The Odyssey detects a wave of radiation from the stargate sweeping across the planet, and beams SG-1 out just in time. All of the people on the surface of the planet, including Ori forces are killed.
SG-1 quickly deduces that the radiation was from the Ancient weapon on Dakara. Teal'c is upset that the Jaffa nation has decided to begin mass murdering in order to fight the Ori. They quickly realize they have a windfall on their hands: an Ori ship on the planet with no Ori soldiers to guard it. They beam down to learn what they can learn about the ship before Ori reinforcements arrive.
Meanwhile, Bra'tac has arrived at the SGC to tell General Landry about the Jaffa's new strategy, which Bra'tac opposed. Landry decides to visit Dakara and speak to the new Jaffa leader, Se'tak, personally.
SG-1 explores the Ori ship, but they run into problems when a small group of Jaffa warriors arrive to claim the ship for themselves. The Jaffa refuse to compromise, and they capture Mitchell and Teal'c. Several Jaffa motherships arrive, so the Odyssey retreats to avoid detection.
While the Jaffa and the rest of SG-1 are playing cat-and-mouse, Adria appears and captures Vala and Daniel. Adria has some type of device that protected her from the weapon on Dakara. She is happy to renew her acquaintance with her mother, and she wants to know what the weapon was that decimated her forces. Vala and Daniel resist telling her, but she uses her telekinetic and telepathic abilities to force it out of a Jaffa. Adria single-handedly operates the ship, taking off from the surface, destroying the Jaffa ships in orbit, and setting course for Dakara. The Odyssey follows.
General Landry hasn't made much progress in discussions with Se'tak. Se'tak says that although the loss of innocent life is regrettable, the Jaffa have no other course of action against the Ori. Landry steadfastly opposes the tactic as mass murder. This is a thorny moral question, because both sides have their points. The Jaffa are more widely spread throughout the galaxy, so they are suffering more immediate losses than Earth. Landry's position is morally correct, but preaching about what the Jaffa shouldn't be doing while offering no alternatives is not helpful. The SGC has not managed to come up with any effective tactics against the Ori.
Landry is finally reduced to saying that the use of the Ancient weapon violates the agreement between the Jaffa and the SGC, but Se'tak has picked up on democracy quickly and says that he can't be bound by agreements made by previous leaders. The discussion between Landry, Bra'tac, and Se'tak break down when news arrives that the Ori ship has destroyed the Jaffa ships; Se'tak believes SG-1 is controlling the ship, and imprisons Landry and Bra'tac.
Adria brings the ship to Dakara and begins attacking the Ancient weapon. Se'tak orders the Ancient weapon to be used on Dakara and its vicinity, which would kill even people on ships in orbit. (The controllers of the weapon are safe in the control room, where Se'tak, Landry, and Bra'tac are.) On the ship, Carter has been free the whole time and manages to lower the shields so the Odyssey can beam all of SG-1 off just before the weapon hits. Everyone on the ship (all Jaffa) except Adria are killed. It also appears that everyone on Dakara is also killed - it's not clear if the residents were there, because I believe that Bra'tac did make a comment that the planet was evacuated.
Adria continues the attack on the weapon, so Se'tak orders it to be fired again. Landry and Bra'tac manage to escape through the stargate, and the Ancient weapon is destroyed, killing Se'tak and the other Jaffa in the control room.
In the end, Bra'tac and Teal'c lament the loss of Dakara, which was a rallying point for the Jaffa. Reports come in of more planets conquered by the Ori, including Hebridan (last seen in season 7's "Space Race") and Langara (last seen in season 7's "Fallout"); the fact that these are planets we "know" makes this strike much closer to home. What happened to Jonas, for example?
This episode is going to have ramifications for the future, and I don't think any of them will be good. First and foremost, the Ancient weapon on Dakara was destroyed. Unfortunately, this happened after only one successful attack, which didn't manage to do much. I don't know how much the Jaffa thought they could accomplish, because the Ori would certainly come after them quickly, anyway. It was just bad luck that Adria was around to learn the location of Dakara immediately.
The cooperation between the SGC and the Jaffa is breaking down again, in some ways reminiscent of the situation with Gerak's leadership in season 8. The Jaffa really just don't like bending their necks to anyone. It's hard to fault them for this, given their history, but you'd think they'd learn!
Adria, now full grown, appears formidable. She still is completely devoted to the Ori mission, spouting the same propaganda. She doesn't see any problem with forcing people to "choose" the correct religion. She has stated her intention of convincing Vala that Origin is true, which has gotten Vala and her immediate companions a little safety, although she didn't have any problem with a little torture of Daniel. Oddly, she says that the Ori have plans for Daniel. What are those plans, and why Daniel?
So now the SGC have no choice but to find Merlin's weapon somewhere. If only they had a better idea where it was.