After coming to the aid of a crippled alien vessel, Captain Archer brings the ship's crew onboard Enterprise for medical attention. The aliens are a deeply religious people known as the Triannons, and Archer invites their leader, D'Jamat, to dinner. D'Jamat explains that the Triannons regard the Delphic Expanse as the "Chosen Realm" and the mysterious spheres are sacred objects created by god-like beings known as the "Makers." The spatial anomalies, D'Jamat says, are merely "the Makers' breath."
The Triannons' presence seems fairly benign — until D'Jamat approaches Archer and reveals that Enterprise is about to embark on a "glorious mission." D'Jamat explains that his crewmen have taken up positions throughout Enterprise and that their bodies are armed with organic explosives. With a single command, D'Jamat orders one of his minions to detonate his explosive. In doing so, the Triannon sacrifices his life, damages part of the ship and kills one of Enterprise's crewmen. D'Jamat tells Archer that two of his men are positioned next to the ship's warp reactor — the Triannons are hijacking the ship and plan on taking it back to their homeworld. Once there, D'Jamat will use Enterprise's weapons to attack the group of "heretics" that his sect has been fighting for a century.
The situation is dire, but it's about to get even worse: after reviewing Enterprise's records, D'Jamat realizes that Archer and the crew have committed acts of "desecration" by flying through the cloaking barriers of several spheres. In addition to wiping out all of Enterprise's research on the spheres, D'Jamat insists that Archer select one crewmember to be put to death. Sensing an opportunity, Archer selects himself, but insists that D'Jamat execute him in the customary way — via the transporter. Now that the Triannons believe Archer is dead, the captain is able to counter their attack. He disrupts the ship's power and covertly contacts Phlox, who formulates an airborne agent that will neutralize the Triannons' organic explosives. Archer also manages to get through to one of D'Jamat's men, Yarrick. Yarrick's wife is expecting a baby and Yarrick has come to realize that going along with D'Jamat's plan means sentencing both his wife and future child to death. Yarrick agrees to help Archer, and the duo manages to assist Phlox in delivering the explosive-neutralizing agent.
Meanwhile, a convoy of Triannon vessels commanded by D'Jamat's enemies approach Enterprise, poised to attack. As D'Jamat engages the ships in battle, Archer locates Reed and the MACOs and prepares to re-take the ship. Archer and his team manage to overpower the Triannons in Engineering, and Archer reroutes command functions and takes the ship's weapons off-line. Archer contacts D'Jamat on the Bridge and demands that the Triannons stand down. Even though their organic explosives have been neutralized, D'Jamat is not ready to surrender. As the situation grows more volatile, Reed and the MACOs storm the Bridge and defeat the Triannons in a firefight. Archer rushes to the Bridge and asks D'Jamat's enemies to end their attack. Once they see that D'Jamat has been defeated, they move off.
Later, Archer takes D'Jamat and his followers back to Triannon. Sadly, they are in for a devastating sight. Though D'Jamat truly believed that his plan would bring peace to his homeworld, it appears that war has already taken its toll. The fighting has decimated both sides, destroying all major cities and leaving millions dead.