The Enterprise, under Captain Jonathan Archer, sets off on its maiden voyage with a mission to return a wounded Klingon to his people.

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.

Starfleet orders Enterprise to return home when the crew seemingly causes the destruction of an alien planet. However, a visit from Crewman Daniels leads Archer to believe that this disaster was the plot of one of the factions from the temporal cold war.

Daniels and Archer must find a way back to the 22nd century in order to make sure history plays out as it should. Meanwhile, on board Enterprise, the Suliban have taken over the ship, but Reed, Trip, and T'Pol formulate a plan to eject the aliens.

Both the Vulcans and the Andorians make a claim to a small planet and military conflict soon erupts. As the fighting goes on, the Vulcans announce they are willing to discuss cease fire terms. However, Imperial Guard officer Shran believes only Captain Archer can be trusted to mediate the situation, which drags the Enterprise crew into the tense situation.

An alien race known as the Xindi launch an attack on Earth, causing great casualties and massive damage. As Enterprise heads back home, an unlikely source informs Archer about the Xindi and that their next attack will destroy Earth.

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.

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

Earth's embassy on Vulcan is bombed, and the ensuing investigation puts Archer and T'Pol on the trail of a Vulcan religious faction hiding in a treacherous desert.

Archer and T'Pol encounter the Syrrannites, a radical group hiding in the Vulcan desert, while the NX-01 crew contends with Vulcan power ploys.

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.

A human isolationist leader threatens to destroy Starfleet Command unless all aliens leave Earth immediately.