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.

Suffering from damage inflicted in the Romulan minefield and unable to complete repairs on their own, Archer orders a distress call to be put out. A response leads Enterprise to a repair station, which surprisingly has no crew aboard it and is run by computer. Repairs on Enterprise are carried out quite efficiently and quickly, though the price for all this is much higher than the crew could've guessed.

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 Enterprise crew find a small craft drifting in space and are surprised to find it contains a human corpse. More questions arise when the Suliban and Tholians make claims to the craft.

The remnants of an alien ship and two frozen cybernetic bodies are uncovered in the arctic by a research team. These aliens soon thaw out and flee Earth, taking the research team with them. Starfleet orders Enterprise to find them, but the crew aren't prepared for just how dangerous these aliens really are.

Enterprise starts experiencing effects of the spatial distortions pervading the Delphic Expanse, and falls victim to predatory aliens.

A spatial distortion leaves Archer unable to form any new long-term memories. Years in the future, he wakes up one morning and is stunned to learn the outcome of the human-Xindi conflict.

Archer goes to extreme lengths to save an abandoned nest of Xindi-Insectoid eggs ready to hatch.

An attempt to use a Xindi subspace corridor leads the Enterprise crew to a bizarre encounter with their own descendants.

Once the NX-01 finally returns to Earth, the weary crewmen face repercussions of their journeys, both positive and negative.

In defiance of their "father," Arik Soong's Augments devise a heinous plot against the Klingons which will surely lead to interstellar war.

Archer, T'Pol and T'Pau attempt to bring the Kir'Shara — an artifact believed to contain Surak's original writings — to the Vulcan capital, as the NX-01 gets involved in a Vulcan-Andorian military clash.

Enterprise journeys to Babel with a Tellarite ambassador on board for peace talks with the Andorians, when a distress call from Shran is received.

While Enterprise visits Earth for the launch of Columbia, Phlox is kidnapped and forced to help the Klingons deal with a grave threat toward their species.

In the mirror universe, Commander Archer mutinies against Captain Forrest in order to capture a future Earth ship found in Tholian space.

In the mirror universe, Archer commandeers the 23rd-century Defiant from the Tholians and uses it in a nefarious power grab.