On a mission to investigate an abandoned Xindi vessel on a jungle planet, Archer, Reed and Hoshi succumb to a virus that mutates them into a primal life form.

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

Captain Archer and his crew set out to gain information about the mysterious and antagonistic Xindi race.

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 learns the Klingons have put a price on his head when he is captured by a Tellarite bounty hunter. As Enterprise pursues, a virus causes T'Pol to go into premature Pon Farr.

Archer tells T'Pol the story of when he and a rival named A.G. Robinson were in competition for breaking the Warp 2 barrier.

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.

The Enterprise crew makes first contact with the Vissians, a species with three genders. Trip meets one of the species' third gender, known as Cogenitor, and learns how badly Vissians treat all Cogenitors. Trip attempts to help the Cogenitor, even though it interferes with Vissian culture.

When militants take over a world, the Enterprise crew move to evacuate Denobulan geologists that are deep underground. Meanwhile, Phlox has to save a dying Antaran that refuses treatment due to the history of their races.