Admiral Forrest learns from Ambassador Soval that the sacred Vulcan monastery at P'Jem has been destroyed, a result of Captain Archer's discovery of a surveillance station beneath the sanctuary and his sharing the finding with the hostile Andorians. Blaming both Archer and T'Pol for the incident, the Vulcan High Command decides to remove T'Pol from her position on Enterprise, and arranges to send a ship to take her back to Vulcan.
Upon delivering the news of her reassignment, Archer is disturbed with T'Pol's nonchalant attitude towards her imminent departure. But since she has two days left as part of his crew, he asks her to accompany him on a trip to the capital city of Coridan, a planet already familiar with Vulcans but not humans. Piloting a shuttlepod to the planet's surface, Archer and T'Pol suddenly come under attack by an unidentified aircraft and are taken prisoner. Held inside an old shanty in an unknown location, Archer learns their captors are Coridan rebels who are mounting a coup against the current government, which is kept in power by the Vulcans.
While Archer and T'Pol struggle unsuccessfully to escape their restraints, Commander Tucker is informed by the Coridan Chancellor that the kidnapping is the work of a radical faction who must not be negotiated with, but that the government is doing everything in their power to find the crewmen. Tucker won't sit on his hands, though, so he orders the crew to run scans for the shuttlepod. Just when they locate it amidst a "shantytown" just outside the capital, they are hailed by Traeg, one of the abductors, who demands weapons in exchange for the hostages. While Tucker and Reed consider their best course of action, the Vulcan ship Ni'Var arrives a day early to pick up T'Pol, but then learns of the kidnapping from Tucker. Visiting Enterprise to discuss the situation, the Vulcan captain, Sopek, opts to mount a quick, decisive rescue mission, advising the human crew to stay out of the way. This worries Tucker and Reed, so they discreetly take a shuttlepod to the surface. As they search the Coridan shantytown for their crewmates, they are themselves ambushed and kidnapped. It turns out their captors are Shran and Tholos, two of the Andorians they came to blows with at P'Jem, and they actually abducted Tucker and Reed for their protection. Shran explains that the Andorians are in league with the Coridan rebels, supporting their fight against the Vulcan-backed government, a government he claims to be corrupt. But since the P'Jem incident, Shran has lost sleep over feeling indebted to Archer, so he wants to secure the captain's freedom from the rebels. Shran and Tholos have a plan to break Archer and T'Pol out of the rebel compound, but they would be vastly outnumbered, so they let Tucker and Reed have their weapons back and come along.
The humans and Andorians work together to overcome the guards and infiltrate the rebel compound. Just when they are about to reach Archer and T'Pol, the place is also raided by heavily armed Vulcan commandos, led by Sopek. Suddenly the Enterprise crewmen and Andorians are caught in massive crossfire between the Coridans and the Vulcans. But Tucker and Shran manage to slip by and reach Archer and T'Pol. After helping to untie the hostages, Shran gives Archer back the scanner that contained the incriminating evidence from P'Jem — his debt is now repaid in full. The Vulcans overpower Traeg and the other Coridan rebels and are then met by the humans and the Andorians. While the Vulcans and Andorians face off in intense distrust, weapons trained on each other, Traeg regains consciousness and aims a gun at Sopek. T'Pol immediately throws herself at Sopek and takes a plasma bullet in her flank. After the Andorians return fire and put Traeg down for good, Archer takes the severely injured T'Pol in his arms, refusing to turn her over to the Vulcans, and leads his crewmates back to the shuttlepod.
While T'Pol is treated by Dr. Phlox in Sickbay, Sopek visits and learns the prognosis is uncertain. Archer appeals to Sopek to let her have a second chance, given her heroic sacrifice. He agrees to bring the matter up with the High Command and leaves. When T'Pol awakens, Archer tells her the odds are pretty good she'll be on Enterprise a while longer.