The Enterprise crew alters course to investigate the mystery of Terra Nova, a legendary Earth colony whose inhabitants mysteriously disappeared decades ago. But when they arrive, they confront descendents of the colonists who have become more alien than Archer could ever have imagined.

The Enterprise crew is dispatched by Starfleet Command to assist Fortunate, a human freight vessel that has been attacked by Nausicaan pirates. On arriving, they are surprised to find that Fortunate's crew is resistant to Archer's efforts to help them and determined to seek revenge against their attackers, no matter the repercussions.

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.

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.

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.

When Trip suffers a catastrophic injury, his only hope for survival is a transplant from a "mimetic symbiont" which Phlox grows from one of his exotic creatures.

Two high-ranking Xindi offer to stop the launch of their superweapon if Archer can prove they've been manipulated. Meanwhile, the crew mourns their lost mates.

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

A xenophobic faction of humanity threatens to undermine talks to form a new coalition of planets.