Captain Archer and Commander Trip Tucker, after finding the Vulcan star maps incomplete, talk Sub-Commander T'Pol into taking a trip to P'Jem, a Vulcan monastery. When Archer, Tucker, and T'Pol arrive at P'Jem, they find the Vulcans have visitors: the Andorians. As one of the most significant of the first season episodes, the events of "The Andorian Incident" would continue to resonate into the fourth season. This would, in particular, affect T'Pol and her family.
On board the Enterprise, Archer tells T'Pol that while going through the charts he found a remote outpost on a planet a few light years off their current heading. He continues by saying that he would like to visit this Vulcan monastery, P'Jem. T'Pol describes it as an ancient Vulcan spiritual retreat, a place for kolinahr and peaceful meditation, and notes that she will need to find the proper protocols for the visit.
However, unbeknownst to either of them, the monastery has already been captured by four Imperial Guards of Andoria. En route, T'Pol explains the strict protocol - they should not speak to anyone unless spoken to first, talk to anyone who appears to be meditating, or touch any relics or ornamentation. However, once they arrive, evidence is found of the Andorian attack. A Vulcan monk tries to send them away, but Archer spots the reflected form of an Andorian. Although the away team manage to subdue him, they are captured by a larger group of armed Andorians, led by Shran. Shran interrogates Archer asking if they have brought more surveillance equipment for the Vulcans. He believes that the Enterprise is too well-armed just to be visiting, believing their presence confirms his theory about the monastery.
The Andorians lock up the away team with the Vulcan monks. The monks then explain that Andoria is the neighboring system to Vulcan and that they have negotiated a peace treaty. However, the Andorians believe that P'Jem holds a long-range sensor array. The monks say that the Andorians have visited twice before and left within a day both times. The arrival of the Enterprise and T'Pol has unfortunately amplified their suspicions. During interrogation, and wrongly disbelieving Archer's protestations of ignorance, Archer is beaten. When the Enterprise attempts to contact the away team, Shran warns them not to interfere and destroys the communicators.
Upon Archer's return, the monks relent and take Trip to an ancient transmitter in the catacombs, passing a door that leads to the Reliquary, where the most precious artifacts are kept. After repairing the transmitter overnight, Trip manages to send a signal to Enterprise to tell them to wait. Reed and some security guards later transport into the tunnels, taking out most of the Andorians with explosive charges and phaser fire. Shran escapes into the Reliquary, where a fire-fight reveals a large circular door. Archer manages to open the door, which reveals the long-range sensor array. Now, the Vulcans have been exposed, Archer lets the Andorians go with T'Pol's palm scanner as evidence of the deception and the Enterprise leaves. Shran remarks that he is in Archer's debt.