The episode begins with Daniel, Sam, Teal'c, Mitchell and Vala who are on a recon mission on one of the planets that has fallen to the Ori. They are in the street listening to a speech made by one of the Ori followers when Adria (who is now a mature woman) steps out to address the people with Ori propaganda. In orbit the Odyssey suddenly picks up an energy reading coming from the surface of the planet. The reading turns out to be a wave of radiation emanating from the stargate and its spreading fast. As a precaution all SG-1 members are quickly beamed aboard the spaceship. Shortly after they are beamed aboard, they discover that there are no more life signs to be found on the planet surface. Daniel tries to comfort Vala, who has to deal with the possibility that her daughter is dead. However, Vala pretends nothing is wrong and that she is relieved with what happened.
Meanwhile, back at Stargate command, Bra'tac comes through the stargate to warn general Landry about something that threats millions of lives. When a team returns to the surface from the ship, there is no one left. Strangely, the only things remaining are the clothes the people were wearing, which are lying in the streets. Together with the information that the wave emanated from the stargate, this causes SG-1 to fear the worst: that the weapon on Dakara used to defeat the Replicators has been adjusted to serve as a weapon against both the Priors and the human armies who have fallen to the Ori. At Stargate Command, Bra'tac confirms this story with general Landry, who informs him he has already heard it from SG-1. Bra'tac explains he has tried to stop their new leader Sa'tac and the council from using the weapon but that the more he spoke out, the more he became isolated. General Landry demands to speak to the council.
Back on the Odyssey, Carter informs the other team members that there is now an unmanned and unguarded Ori ship on the surface, posing a unique opportunity. They then beam down to the Ori ship and split up in groups. Vala gets teamed up with Daniel and when they're alone she asks him what he meant back on the Odyssey when he told her he knew how she felt in regards to her loss of Adria. Daniel tells her the story of Sha'ree, how she was taken as a Goa'uld host, how he joined SG-1 in hopes of getting her back and how he ultimately failed to do so. He tells her that in a small way he feels relieved too, that's she's no longer suffering at the hands of the Goa'uld.
In another part of the ship, Teal'c and Mitchell stumble upon a power generation chamber and they decide to plant some C4 in it in case it turns out to be necessary to disable the ship. Sam, who has been exploring the ship by herself, comes upon what she thinks is the ship's bridge, which has a control chair similar to the one the weapon in Antarctica has. Unfortunately this probably means the chair is keyed to the Prior's unique brain physiology and they'll be unable to fly the ship. So Sam tells Mitchell she will try to get some information out of the ship's database before the Ori come back for the ship and they have to blow things up. When Mitchell is on the radio with Sam, he and Teal'c suddenly hear the sound of marching footsteps and are instantly faced with a weapon's showdown with a group of Jaffa warriors. With weapons raised and neither side budging, they discuss who has the right to lay claims to the ship. When the lights on the ship suddenly dim and Teal'c and Mitchell are ambushed by another Jaffa from behind, Mitchell gets hit by a shot from a zat'ni'katel and Teal'c is faced with a shooting with the other Jaffas. Sam, having heard the shooting, requests the Odyssee to perform an emergency beam-out, but they are unable to get a lock on them. Sam thinks she might have accidentally activated the ship's shields and goes to work to undo it. Meanwhile however, Teal'c too gets downed by a zat'ni'katel, and three Ha'tac vessels enter the planet's orbit, forcing the Odyssey to move out of range.
General Landry and Bra'tac arrive at and meet with Sa'tac. Landry informs him that the use of the weapon violates their prior agreement, but Sa'tac tells Landry he longer feels bound to that agreement, now that much has changed with facing an enemy never encountered before. He says that using the ancient weapon, the costs of victory is great, but that the cost of defeat would be even greater. On the Ori ship, Daniel and Vala too are captured by the Jaffa and when Daniel tries to convince the Jaffa that they should be working together, Adria suddenly walks in and kills the Jaffa by telekinesis. She is happy at seeing her mother again and tells her she's missed her, even though she was told to forget about her, because her mother abandoned her, and didn't care about her. Adria tells Vala she was saved from the weapon by her necklace, which holds a piece of the holy city of Celestus, and it protects her and keeps her safe.
When Mitchell is being interrogated about what the remote C4 detonator is for, Sam manages to create a distraction by shutting down the ship's power from the bridge. At the same time Vala tries to convince Adria she is doing the wrong thing, Adria reanimates a Jaffa, to get to know the origin and location of the weapon that was used against her followers. Unable to resist her powers, he finally mutters the word "Dakara." Meanwhile, Sam makes use of the distraction she created, and manages to free Mitchell and Teal'c. They contact Daniel and Vala who are still with Adria, and inform them they're leaving the ship, but Adria uses her powers and reactivates the ship, lifting off to go to Dakara, and easily destroys the three Ha'tac ships when they encounter them in orbit.
Alerted by these events, the Odyssey comes back into range and discovers the Ori ship has left the planet, with no signs of SG-1. They come to the conclusion they must still be on the ship and are probably headed towards Dakara, before pursuing it. Back on Dakara, general Landry and Bra'tac are held prisoner by Sa'tac because he too has heard the news of the ship lifting off, and heading towards Dakara. With no reason to think anyone was left alive, he is convinced that SG-1 is in command of the ship and has destroyed the Ha'tac vessels. Daniel and Vala learn from Adria that soon many many more Ori ships will arrive and that the galaxy will likely be converted within the year.
When the ship arrives at Dakara, Teal'c and Mitchell cannot allow it to fire upon the planet, and are forced to detonate the C4 they planted and destroy the ship. However, when Mitchell throws the switch, nothing happens. It turns out Adria used her powers to prevent the detonation. Down on the planet, the council aim and fire their weapon at the Ori ship, convinced it's being controlled by SG-1, with the plan of destroying the Jaffa weapon. Sam manages to disable the shields of the Ori ship, so the Odyssey can beam SG-1 out, and manages to enter hyperspace just before the deadly wave reaches them. However, with Adria unaffected by the wave, due to her necklace, she fires repeatedly at the ancient weapon on the planet’s surface. Just before escaping through the stargate, Landry and Bra'tac look around and witness the ancient weapon being fired upon by the ship's energy beam. Back at Stargate Command, Teal'c informs them that a cargo ship went back to the planet, only to witness complete devastation on Dakara.
With the ancient weapon now gone and the Jaffa nation fractured, things are looking more and more grim, and Merlin's device seems to be their only hope now...Read the full recap
Teal'c: A great Jaffa once said: exalted is the warrior who chooses victory without battle.
Mitchell: Winning shows strength. Winning without fighting shows true skill.
Teal'c: Hmm... you're a student of ancient strategies.
Mitchell: No, Landry said it to me. I think he was quoting Sun Tzu... or it could have been Dr. Phil
Landry: (to Walter) Sometimes you make the right decisions, sometimes you make the decision right.
Walter: (nods) Patton.
Landry: That one's Dr. Phil
Vala: There's nothing to be gained by second-guessing yourself. You can't remake the past, so look ahead... or risk being left behind.
Bra'tac: She displays the wisdom of a battle-seasoned warrior.
Daniel: She's a mother. Close enough.
Bo'rel: We achieved this victory, therefore we claim the spoils.
Teal'c: What you have done is sacrifice the lives of thousands of innocents.
Bo'rel: No one is innocent who joins with my enemy.
Mitchell: They were invaded by an army with massively superior firepower.
Bo'rel: They should have resisted.
Mitchell: So die at the hands of the Ori or die at the hands of the Jaffa. Some choice.