Archer sends an away team to a habitable, luscious planet for observation. But when a storm occurs, the team begins to experience paranoid delusions.

Archer and the crew are disappointed to discover that T'Pol has been ordered by the Vulcan High Command to leave Enterprise--and equally frustrated at her seeming indifference to leaving their ranks. T'Pol's last mission as a Starfleet officer, however, proves eventful when she and Archer are kidnapped by a militant faction on an alien planet.

Enterprise encounters a group of Vulcan civilians who have split off from the normal way of Vulcan life in an effort to explore their emotions. T'Pol is disturbed by the new visitors and warns the Captain that all attempts in the past to integrate Vulcan emotions into their lives has proven disastrous. Meanwhile, a message from Admiral Forrest leaves the Captain with the difficult task of trying to convince one of the visiting Vulcans to call home to speak with his dying father.

While exploring a planet, Archer and Mayweather enter a “military zone” and are detained in an internment prison by an alien race called Tandarans, who are at war with the Suliban. While the Enterprise crew's previous encounters with the Suliban have been disastrous, Archer and Mayweather find themselves sharing a cell with some Suliban detainees who they believe may be wrongly imprisoned.

Archer learns the Klingons have put a price on his head when he is captured by a Tellarite bounty hunter. As Enterprise pursues, a virus causes T'Pol to go into premature Pon Farr.

Archer finds himself face-to-face with Degra, the designer of the Xindi superweapon, and tries to get him to reveal its location.