A Prior is preaching to the people of one of their villages as SG-1 secretly looks on from the crowd. Adria, now an adult, comes out to address the villagers. She seems to sense something and leaves. In orbit, the Odyssey senses a wave of energy emitting from the gate and beams SG-1 out. They detect no life signs on the planet--the thousands of residents have been instantly killed.
Daniel tries to comfort Vala over the seeming death of her daughter, but Vala is more relieved than anything. On the planet, research teams from Earth determine there's no residual chemical or biological residue, and the effect only destroyed living tissue. They realize what the weapon was.
At SGC, they get an incoming wormhole and Bra'tac arrives. The elder Jaffa has dire news for Landry--the Jaffa used the weapon on Dakara to wipe out biological material much as it was used against the Replicators. Bra'tac spoke out against the plan, initiated by the new Council leader Se'tak. Meanwhile SG-1 check out the now-empty Ori ship on the planet. They split up and Daniel explains he knows what Vala is going through since his wife was taken by the Goa'uld.
Mitchell and Teal'c find the ship's engine and attach C-4 charges while Sam finds the control room with a chair similar to the one in Antarctica. Sam starts to check the database but Teal'c and Mitchell encounter Bo'rel of the Free Jaffa. Bo'rel demands access to the ship because they achieved the victory and he is unconcerned about the loss of innocent lives. A firefight breaks out and Mitchell is stunned. Teal'c takes on the others and Sam calls for beam out, but the Odyssey can't get a lock on them. Teal'c is stunned while Sam contacts Vala and Daniel. She reveals she accidentally activated the shields, blocking the transporter. While Sam tries to disengage the shield, three Jaffa ships arrive in orbit and the Odyssey is forced to retreat to avoid detection. Se'tak is declaring the attack on the Ori a success when Bra'tac and Landry confront him. Se'tak plans to continue using the weapon no matter the cost.
Bo'rel interrogates Teal'c and Mitchell but isn't convinced by Mitchell's denials that the rest of the team has retreated back through the gate. He broadcasts a surrender request throughout the ship. Daniel contacts them to suggest they work together but Bo'rel refuses and then a Jaffa patrol finds Daniel and Vala. However, Adria arrives and disposes of the Jaffa patrol and prepares to dispose of Daniel.
Vala persuades her to stop and Adria reveals she had a piece of the Holy City of Celestis that protected her. Adria says they won't be separated and embraces her mother. Bo'rel interrogates Mitchell and messes with a remote device to the charges they put on the power core earlier. He ends up cutting power to the ship.
Adria demands to know what happened to the people on the planet. She tries to mentally interrogate Daniel but he's able to resist. Thwarted, she interrogates one of the Jaffa and finds about the Dakara weapon, throwing back Vala when she tries to interfere. Sam shows up to take out the Jaffa guarding Mitchell and Teal'c.
Landry warns Se'tak that their alliance is at risk, but the Jaffa leader warns they are the ones fighting the battle while Earth remains untouched. When Landry asks why they are testing the weapon on a human rather than Jaffa world, Se'tak ends the discussion.
Sam reveals there's someone else on board who activated the shields. The engines start up and the free SG-1 team heads for the control room to override. The Ori ship lifts off and readily dispatches of the three Jaffa ships, while Se'tak tells Landry of the news. Se'tak believes SG-1 is responsible and imprisons him and Bra'tac.
Sam and the others get to the control room while Adria reveals that Vala's "husband" is still alive as he was on another planet. She warns that the galaxy will be converted within a year when the other Ori ships arrive. Teal'c and Mitchell go to search for Daniel and Vala and run into Bo'rel's team.
Vala isn't ready to embrace Origin but Adria believes she'll bring her around… eventually. Daniel suggests she give people free will but Adria would rather remove all doubt through any means necessary.
Teal'c confronts Bo'rel and tells him they aren't aware of who is controlling the vehicle, and they should ally. Bo'rel agrees to a temporary alliance.
Adria isn't interested in listening further to Vala and then announce they've arrived at Dakara. Se'tak is aware of the ship's arrival and accuses Landry of conspiracy, and says they will lay siege to Earth to recover the ship. Mitchell prepares to detonate the C-4 charges even though it may destroy them all, but they realize they have no choice.
Mitchell activates the charge but nothing happens--Adria has telekinetically disabled the charges. The Odyssey has been following the Ori ship but still can't beam them out. Se'tak takes them Landry and Bra'tac to the Dakara weapon and prepares to activate it in a wave to destroy everyone on the ship.
Vala offers to go with Adria and listen to what she says, but Adria refuses and says she has plans for Daniel. Se'tak's people activate the weapon while Sam drops the shields. The Odyssey beams out SG-1 and gets clear just in time as the weapon's wave sweeps over the ship. Adria is once again unharmed and activates the ship's weapons, bombarding the planet. Bra'tac gets Landry out and they head for the gate while the complex comes down around Se'tak, destroying the weapon.
Back on Earth, Teal'c announces they have news that Dakara is no more, while five more planets have fallen to the Ori. Landry orders them to find the Merlin device, their only hope. Bra'tac is concerned that without Dakara, the Jaffa factions will break up. Vala offers a few reassuring words but the future looks grim.