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.