When Trip is dispatched to assist a Xyrillian ship with its power source problems, he is delighted to have a friendly encounter with one of the ship's female engineers. However, shortly after returning to Enterprise, he discovers that their seemingly innocuous interaction has led to a surprising result.

Captain Archer and the crew discover a fully inhabited, civilized though less advanced Earth-like planet. Disguised to look like its inhabitants, they pay the planet an exploratory visit where they learn that a pernicious illness is afflicting the local population. As Archer seeks to help them find the malady's source, he finds himself in a close encounter with a comely female alien.

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.

In need of fuel, the Enterprise arrives at a Quonset mining colony for deuterium supplies. They discover that Klingons are forcing the colonists to give up all their deuterium. Archer and the rest of the crew work to train the colonists so they can fight back against the Klingons.

When a lethal neutronic storm approaches faster than Enterprise can escape, the crew take shelter in the maintenance shafts inside the warp nacelles. They also provide refuge to a group of aliens, who aren't exactly honest about themselves.

The NX-01 gets closer to a showdown with the Xindi when Captain Archer takes on an enigmatic passenger: a beautiful slave named Rajiin.

Archer and T'Pol travel back in time to 2004 Detroit to stop a Xindi plot.

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

Arik Soong leads his band of Augments to a medical facility where hundreds of genetically enhanced embryos are still stored, intending to retrieve them and bring them to life.

Non corporeal aliens study the Enterprise crew as they respond to a fatal viral infection brought on board from an away mission.

Archer visits Shran's icy homeworld to find an Andorian subspecies called the Aenar, to determine their connection to the marauder destroying ships in the region.