Gerak (now a Prior) addresses the Jaffa Council and Teal'c accuses him of promising his mind. The two debate and Teal'c warns that Orrin has informed them the Ori feed on the energy of their worshippers. Gerak claims the Ori are true gods unlike the Goa'uld, and gives a demonstration of the powers they have given him. At SG Command, Lam informs Landry that the plague is spreading and casualties at the base are increasing. The CDC reports more cases in Mexico and Canada.
Mitchell meets with Jolan and Lord Haikan who reveal that the Ori sent them on to a mission to eliminate harmless non-believers, and they are now convinced to turn against their "gods." They ask Mitchell for help and he warns them they won't like his answer. Orlin is still working on the cure when Sam tells him his brain is degenerating – not only his memories fading but the knowledge is damaging his human brain. He refuses to write down his knowledge fearing Sam can't interpret it.
Mitchell and Daniel plant a device that will scramble the Prior's power-link to his masters, but they have to scan randomly for the proper frequency. Mitchell warns that someone is going to have to test the Prior to find out – he plans to do it himself. Then they can take a blood sample and use it to find a cure, while they turn the Prior against the Ori. Mitchell asks Haikon to get the Prior as close as possible to the hidden device.
Teal'c and Bra'tac are concerned they have lost the argument with Gerak and must retreat before Gerak retaliates. Teal'c advises they expand on Chu'lak and forment civil war to force the Council's hand. Orlin is struggling to complete the cure despite his deteriorating brain and warns he can't control what little information he retains. Landry meets with the other countries in on the project and demand an accounting. He warns they have no way to stop the virus and there's nothing they can do.
Teal'c and Bra'tac start to gather followers while the Prior arrives to meet with Haikon. The Prior demands to know why the Sodan disobeyed the Ori, while Mitchell uses their cloaking device to get closer. The Prior unleashes his power, revealing Mitchell, while Daniel scans for the correct frequency. As the Prior suspends Mitchell in mid-air and prepares to kill him, Daniel finds the right frequency and Mitchell drops to the ground, then stuns the astonished Prior.
Hammond arrives to meet with Landry, who reports the plague has spread to France and they must prepare for global chaos. The Prior wakes up without his powers but warns the Ori will strike them down…eventually. The Prior remains confident in his beliefs despite their best efforts. At SG Command, Orlin begins to lose coordination and almost releases a deadly sample – he resigns while they secure the spilled sample.
Teal'c and Bra'tac are aboard a fleet of pel'tacs waiting for Gerak to attack, and Bra'tac suggests Teal'c is best suited to leading the Jaffa rather than working with SG-1. In turn Teal'c suggests Bra'tac should lead their people. Teal'c promises that no Jaffa blood will be spilled.
Landry gets more reported cases throughout Europe and Africa and then reassures Orlin they can continue without him. But he does ask Orlin to do one more thing.
Gerak's fleet arrives and Gerak warns they are outnumbered. Teal'c refuses to surrender and suggests a meeting on the nearby planet. Landry arrives on the Sodan planet and confronts the Prior, wondering what he gave up. Landry talks about his own daughter and then brings Orlin, who knows the Prior as Demaris and talks about the man's previous life. Demaris quotes scripture while Orlin points out the Ori have never ascended any of their followers. Then the Prior manages to tap into his powers, choking Landry, and Mitchell is forced to kill him. Before he dies, the Prior warns that the Ori are coming to destroy the Ancients.
Teal'c meets with Gerak and shows him the ruins where Gerak's father gave up his life in battle against the Goa'uld. It was his father's death that led Gerak to rebel against the Goa'uld. Teal'c questions the Ori's godhood and how Gerak sought enlightenment and tried to avoid bloodshed. Teal'c offers his own life to Gerak rather then returning to slavery.
Back at SG Command, Lam reveals that Landry now has the virus. Hammond gives his regards to SG-1 as he heads back to Washington. Lam meets with Landry and reveals Orlin's degeneration is accelerating. They share a family moment over Lam's resentment about Landry keeping his career secret but now she understands. They're interrupted by an unauthorized off world Gate activation. It's Teal'c and Gerak – Teal'c takes Gerak to sickbay where he uses his powers to cure…everyone in the base. The effort causes him to burst into flame due to a fail-safe placed by the Ori.
Three thousand people have died while the news agencies wonder where the disease started. They use the blood from the cured victims to create a vaccine for the other plague victims throughout the world. Then they have a briefing and are sure the Ori will launch a different attempt. Sam visits Orlin at a retirement home, where he is being kept because of the near-total collapse of his mental functions. He doesn't remember Sam but the two share a moment working on a jigsaw puzzle.