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

When the Enterprise comes in contact with an alien vessel transporting stargazers to observe a spectacular stellar event, Archer invites them aboard the ship not realizing that Silik, a Suliban enemy, is among them. Archer quickly realizes that Silik is engaged in a nefarious time-travelling mission and must stop him before he can tamper with the course of history.

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.

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.

Archer and the NX-01 find themselves in Earth's past, with events of World War II altered by the Temporal Cold War.

With Silik's help, Archer hones in on the temporal operative who altered Earth's past and threatens to destroy all of time.