As Enterprise warps through the depths of space, Captain Archer decides to take the opportunity to visit a nearby ancient Vulcan monastery called P'Jem, a sanctuary for meditation and "Kolinahr," or purging of emotion. T'Pol briefs Archer and Commander Tucker on the proper protocols for such a visit, and the three of them take a shuttlepod to the 3000-year-old temple. Something seems amiss as the trio enters, finding it suspiciously unoccupied with damage to the building and the artifacts. A Vulcan Elder informs them they are interrupting Kolinahr and must leave, but Archer notices a reflection in an urn of a strange alien hiding with a weapon. He and Tucker rush the intruder, but then find themselves surrounded and captured by a group of militaristic blue-skinned aliens.
The antennaed invaders reveal their paranoid nature as the leader, Shran, interrogates Archer and accuses him of being involved in a conspiracy with the Vulcans. Left confined in a meditation room with a group of Vulcan monks, Archer learns that the invaders are Andorians, a suspicious and volatile species from a neighboring system who believe the Vulcans intend to invade their homeworld despite a treaty between the two races. The Andorians think the monastery is hiding a long-range sensor array, but the Vulcan Elder insists they have no technology there, and chides Archer for amplifying their suspicions.
Meanwhile on Enterprise, Lt. Malcolm Reed detects an alien vessel on the ground that is not Vulcan. When he tries to contact the landing party, Shran answers Archer's communicator and proclaims the captain a prisoner of the Andorian Imperial Guard, and warns that any attempt to intervene will lead to the hostages' deaths. Reed has no intention of standing idly by, so he researches the Andorian race while preparing a rescue mission. On the surface, Archer presses the Vulcans for options, so the Elder confesses to the existence of an old transmitter within the catacombs underneath the temple. A young Initiate leads Tucker through a secret entrance into a dark maze of passages filled with ancient relics and Vulcan mummies, to the dusty transmitter which Tucker sets out to fix. He manages to send a message to Reed to sit tight while they work out an escape plan themselves.
Despite the Vulcans' resistance to any form of violence, Archer learns the layout of the underground tunnels and formulates a plan. He gets the Andorians to bring him into the atrium with the promise of "information," but then he just babbles useless trivia under the ruse of needing to get away from the Vulcans. Actually he's there to slip a tiny artifact through an orifice in a large face sculpture in the atrium wall. Archer gets brutally beaten by the Andorians, but when Tucker finds the tiny artifact he now knows which passage leads to the atrium. Reed and two other crewmen beam down into the meditation room and go underground to plant explosives behind that face sculpture. The Andorians detect an energy surge and new bio-signs, but before they can react the atrium wall explodes and they get into a firefight with the rescue team. Reed manages to stun two Andorians, but Shran and one other escape into the catacombs. Archer arms himself and leads his people in pursuit, with the Vulcan Initiative insisting on going along. They track the Andorians to the Reliquary, where the temple's most sacred artifacts are kept, and enter over the Initiate's objections. They come under attack by the Andorians, with many relics getting destroyed. In the midst of the chaos, Archer finds hidden behind an ornate curtain a high-tech door that seems very incongruous in a place that's supposed to have no technology. Archer finds the controls to open it, and calls for a ceasefire. The humans and Andorians — and T'Pol — are all astonished at what they see: a massive complex filled with sophisticated surveillance equipment and several Vulcan technicians. Obviously the monks have been lying all along about the sensor array, so Archer orders T'Pol to take pictures with her scanner and hand it over to the Andorians, as evidence the Vulcans violated their treaty. T'Pol complies, and also orders Enterprise to allow safe passage for the Andorians. Shran takes the scanner, and on his way out tells Archer they are in his debt.