The episode begins with Commander Tucker and Ensign Mayweather in a shuttlepod gathering readings on one of the Spheres in the Delphic Expanse. Unbeknown to any of the Enterprise crew, they catch the attention of a nearby group of Triannons. Later the Enterprise receives a distress call from the Triannon's ship which reports they have been damaged by a spacial anomaly. The Enterprise takes them aboard to provide aid and sends a crew to repair their ship. D'Jamat, the leader of the group, has dinner with Captain Archer and Sub-commander T'Pol where he explains they have been on a year long pilgrimage to the Sphere. They believe deities, called "The Makers," constructed the Spheres to transform the Delphic Expanse, which they call "The Chosen Realm," into a paradise. T'Pol and D'Jamat start a heated discussion over the Triannon's beliefs. Meanwhile, one of the Triannon women approaches Dr. Phlox to discuss a delicate medical issue.
Some time later, D'Jamat informs Archer that several members of his group have been implanted with organic explosives and placed themselves at key points in the ship. He says they are willing to detonate themselves on his command and demonstrates this by having one of his group do so, killing an Enterprise crewwoman and injuring several others. D'Jamat demands Archer turn over control of the ship or it will be destroyed. Having little choice, Archer submits. After establishing control of the Enterprise D'Jamat sets a course for his home world and explains to Archer that he intends to use the Enterprise to deliver a decisive blow in a religious civil war that has embroiled his planet for a century. D'Jamat has also examined the ships records and found the Enterprise to have examined three Spheres, which are severe violations under his faith. His religion dictates he should put the entire crew to death and destroy the Enterprise, but because the Enterprise crew risked themselves to help his group, and he likes Archer, he will only erase the data collected and require that Archer pick one crew member to be held accountable.
While Archer is contemplating his decision he recognizes a Triannon named Yarrick as the spouse of the woman who approached Dr. Phlox. He reveals that Dr. Phlox informed him that Yarrick's wife wants an abortion because she has lost faith in D'Jamat and does not want her child fighting in his crusade. Archer say he got the impression Yarrick feels the same, but Yarrick rebuffs him. Yarrick then goes to his wife and she press him on his doubts over D'Jamat's leadership. Archer tells D'Jamat that he has selected himself to be killed, but requests it be done using the device they use for "executions." That device turns out to be the transporter, which T'Pol uses to beam Archer elsewhere on the ship. Archer then contacts Dr. Phlox and they develop an airborne agent to neutralize the Triannon's organic explosives. Archer confronts Yarrick and convinces him to help disperse the agent throughout the ship. During their conversation Yarrick reveals the source of the Triannons' religious civil war is a dispute over whether it took the Makers nine days to construct the Spheres or ten days. Meanwhile, the Enterprise encounters a group of ships from the other Triannon faction and they enter into battle. During the battle, Yarrick releases Dr. Phlox's agent enabling Archer and the crew to retake control of the ships systems. They eventually subdue D'Jamat on the bridge and end the battle.
In the brig, D'Jamat remains convinced his actions were justified to bring peace to his planet and that the resulting deaths are insignificant in light of the "Sacred Truth." Archer then says he will show D'Jamat "some truth" and takes him down to his planet, where it is learned that after D'Jamat's pilgrims departed on their journey the war escalated, leaving millions dead and every major city destroyed. The episode ends with Archer looking over a ruined Triannon city and telling D'Jamat that this desolation is the peace his faith has brought.