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 crew discovers a new planet with two races, one in desperate need of medical and scientific assistance. In the course of trying to help, Dr. Phlox recalls his own Denobulan past to address the ethical dilemmas that arise in the present.

Tucker and Reed set out on a mission in a shuttlepod, as Enterprise is busy investigating an asteroid field. Disaster strikes while the pair are away, leaving the shuttlepod damaged and the warp drive inoperable. They manage to make it back to the rendezvous coordinates only to discover Enterprise was apparently destroyed when it crashed into an asteroid. With the ship seemingly no more, the pair are left abandoned in the middle of nowhere with only a few days of air remaining.

Enterprise encounters Ferengi pirates who use a booby-trapped artifact to gas the crew into unconsciousness, then pillage the ship for treasures. But they haven't counted on Tucker, who happens to be in the decon chamber and avoids the gas, and attempts to win back the ship from the pirates.

A strange, alien creature comes aboard Enterprise, and captures several crew members in its cocoon-like web. With her crewmates' lives in jeopardy, Hoshi faces her biggest challenge yet, in trying to communicate with the lifeform, in order to return it to its home planet.

Archer, Hoshi, Travis, Malcolm and Trip have decidedly different experiences during shore leave on Risa. Meanwhile, on Enterprise, Phlox enters his annual hibernation cycle.

When attempting to explore a new planet, Enterprise triggers a cloaked mine. While the crew deal with the resulting damage, it's discovered another mine is stuck to the hull. During Reed's attempt to disarm it, a spike is driven into his leg, trapping him out there. While Archer goes out on the hull to help him, the rest of the crew learn they are in a minefield belonging to the Romulan Star Empire, who demand Enterprise leave or face destruction.

While Enterprise is surveying a black hole in a trinary star system, the stellar phenomenon causes strange effects on the crew.

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.

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.

Noncorporeal aliens possess the bodies of the Enterprise crew.

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.

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.

A powerful telepath makes contact with Hoshi and offers to help Enterprise find the Xindi ... for a price.

When a settlement of humans living a 19th-century Western lifestyle is discovered on a Delphic Expanse planet, Archer and crew set out to learn how they got there.

Religious zealots hijack Enterprise to use it as a weapon against the enemies of their faith.

As Archer tries to unravel the mystery of a rescued alien, long-simmering feelings explode among his senior officers.

Archer sets out on a suicide mission to destroy the Xindi superweapon as Enterprise faces a brutal attack.

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

Archer puts his life on the line in a risky gambit to intercept the Xindi superweapon and disarm it from within.

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.

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