SG-1 meets with a village that has been visited by an Ori prior but were not threatened. The leader, Tevaris, wishes to hear more but hides the team when the Prior arrives. Tevaris agrees to hear more and the Prior pulls back his hood to reveal he's… Daniel.
Back at SGC, the team meets with Landry and believe Daniel was brainwashed into becoming an Ori. They return to the planet and beam Daniel up, where he claims that he's pretending to be a Prior as part of a plan with Merlin, or at least the memories of Merlin in his head. SG-1 is skeptical and Daneil explains that he needed to be made a Prior so he can steal an Ori ship back to their galaxy with the weapon on board to destroy hem. He wants them to shut down the wormhole blocking the supergate.
Sam explains the situation to Landry and Jack, and they all have to consider if Daniel has been compromised and it's a trap so the Ori can bring in more ships. Jack goes to visit Daniel who explains that once Merlin's influence is gone, Daniel will revert to normal but he can't fly the Ori ship. Adria is close to finishing Merlin's weapon and will be able to complete it without Daniel's assistance. Jack isn't convinced, and Teal'c goes in to talk to Daniel and wants to know why Adria isn't suspicious since he stopped working on the weapon to preach. Daniels says that Adria stopped him from working on the weapon. Teal'c is convinced but Woolsey arrives to tell them that to reveal the government doesn't believe Daniel and has ordered his immediate termination.
Vala meets with Daniel and explains the situation with Woolsey, and claims she has a plan. Daniel is skeptical and Vala tries to explain that if the situation was reversed Daniel would be skeptical.
Jack is furious over Woolsey's plan but the government agent notes they can't restrain him forever. Landry suggests they wait until Merlin's influence ends and Daniel reverts to normal, but Jack notes that if that happens they can't have him pilot the Ori ship. They figure Daniel will tell them the ship's location so they can get to it but Daniel insists he's the only one who should be going. Daniel finally tells them where the ship is located and there is a Prior aboard but he spends his time preaching to the masses, and Daniel has given Sam the info she needs to fly the ship. Woolsey reluctantly agrees to the plan then tells Daniel he'll be frozen at the Antarctica base until his intel is confirmed. Woolsey prepares to beam Daniel out but the teleport malfunctions and Daniel breaks free then takes out the guards and holds Woolsey prisoner.
Jack and Landry are talking when Woolsey is beamed down and Jack is beamed up to Odyssey by Daniel. Daniel needs Jack to complete his plan and breaks orbit. Meanwhile SG-1 go after the Ori ship where they are attacked by guards. After disposing of them, they secure the bridge and jump into hyperspace.
Jack talks to Daniel who explains he's afraid SG-1 won't be able to complete the mission but is still working toward his plan against the Ori. SG-1's ship emerges from hyperspace near the supergate as Vala activates Merlin's weapon but an Ori ship is waiting for them at the supergate and guards burst in: Adria has arrived and shut down all their defenses.
Jack and Daniel arrive at the supergate and realize what has happened to SG-1. They're cloaked so Adria can't detect the ship, but Daniel beams over and convinces Adria he's still working for her and the Ancients didn't intervene once the weapon was completed. He then attacks her using the anti-Ori device and knocks her out. Daniel is weakening and frees SG-1, then asks Jack to call the Daedalus which is standing by. SG-1 activates Merlin's weapon while Jack has the wormhole shut down. SG-1 returns to the bridge to find that Daniel has reverted to human. They call Jack to beam them out, leaving Adria behind. The Ori ships enters the hypergate and disappears.
Daniel wakes up in sickbay and the team wonders how they'll know the weapon worked. They're left to wonder if the Ancients wanted them to succeed or not. Teal'c warns that even if the weapon worked, they still have to deal with the Priors and their soldiers in this galaxy. They're still cloaked but Sam calls them to the bridge when she sees the supergate reactivate and Ori ships come through. The team wonders if they've done the right thing.