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

The Enterprise crew alters course to investigate the mystery of Terra Nova, a legendary Earth colony whose inhabitants mysteriously disappeared decades ago. But when they arrive, they confront descendents of the colonists who have become more alien than Archer could ever have imagined.

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 an uncharted planet, Enterprise crew members encounter a group of aliens who are hunting down indigenous creatures for recreation. During their exploration, Archer is mesmerized by visions of an elusive, yet familiar woman who needs his help.

Enterprise encounters Ferengi pirates who use a booby-trapped artifact to gas the crew into unconsciousness, then pillage the ship for treasures. But they haven't counted on Tucker, who happens to be in the decon chamber and avoids the gas, and attempts to win back the ship from the pirates.

While exploring a crashed vessel on a desolate planet, the Enterprise crew is haunted by some ghostly figures, and they encounter an alien race that has survived despite insurmountable odds. Trip helps repair their derelict vessel and is befriended by Liana, an attractive humanoid alien who develops feelings for him.

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.

A strange, alien creature comes aboard Enterprise, and captures several crew members in its cocoon-like web. With her crewmates' lives in jeopardy, Hoshi faces her biggest challenge yet, in trying to communicate with the lifeform, in order to return it to its home planet.

Enterprise is sent to the planet Mazar to pick up a Vulcan ambassador who has been expelled for misconduct.

When Archer and Trip are invited to a desert-like planet by an alien leader, they discover he is a terrorist who has lured them there under false pretences. Meanwhile, T'Pol, while in command, faces a tough decision when she cannot locate Archer and Trip in the desert.

Archer, Hoshi, Travis, Malcolm and Trip have decidedly different experiences during shore leave on Risa. Meanwhile, on Enterprise, Phlox enters his annual hibernation cycle.

After Archer and Trip become curious about a visit she made to a Pennsylvania mining town called Carbon Creek, T'Pol explains to them that Vulcans actually had their first contact with humans in 1957. That year, a Vulcan ship crashed on Earth and three crew members survived, including T'Pol's great grandmother. They pose as humans in Carbon Creek and take on jobs while waiting for rescue and soon find themselves becoming more involved with the town's residents.

Trip boards an alien cargo vessel to help repair a stasis pod, which holds a beautiful woman in suspended animation. When the woman accidentally wakes up, she reveals she's not a passenger, but a prisoner.

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.

As Archer tries to unravel the mystery of a rescued alien, long-simmering feelings explode among his senior officers.