After Archer and Trip become curious about a visit she made to a Pennsylvania mining town called Carbon Creek, T'Pol explains to them that Vulcans actually had their first contact with humans in 1957. That year, a Vulcan ship crashed on Earth and three crew members survived, including T'Pol's great grandmother. They pose as humans in Carbon Creek and take on jobs while waiting for rescue and soon find themselves becoming more involved with the town's residents.

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 find a small craft drifting in space and are surprised to find it contains a human corpse. More questions arise when the Suliban and Tholians make claims to the craft.

Suffering from damage inflicted in the Romulan minefield and unable to complete repairs on their own, Archer orders a distress call to be put out. A response leads Enterprise to a repair station, which surprisingly has no crew aboard it and is run by computer. Repairs on Enterprise are carried out quite efficiently and quickly, though the price for all this is much higher than the crew could've guessed.

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.

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.

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.

Enterprise visits a planet where an Interspecies Medical Exchange conference is being held. Dr. Phlox tries to obtain research on a terminal disease from the Vulcan contingency, without revealing T'Pol has been infected by it.

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.

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.

In a Klingon tribunal, Archer stands accused of aiding fugitives of the Empire and faces death if found guilty.

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.

Archer and Reed return to a pre-warp society, that is on the verge of war, to recover a lost communicator from an undercover survey mission.

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.

During a solo test mission on Shuttlepod One, Trip is attacked by a territorial alien and forced to land on the night side of a moon. As he tries contacting Enterprise, he discovers his alien foe has made an emergency landing nearby. The two contend with each other as an extremely hot sun rises and threatens both their lives.

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

Hoshi experiences her first transporter experience and strange aftereffects lead her to believe she wasn't reassembled correctly.

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 and Tucker are arrested and placed on a prisoner transport heading for a penal colony, Canamar. They won't have a chance to correct this error, as one of the inmates plots a takeover of the ship.

Mayweather discovers his father has died and that things on his old home, the E.C.S. Horizon, have greatly changed.

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 spends a night in sickbay with Dr. Phlox after Porthos contracts a deadly virus on the Kreetassan homeworld. Crew members suspect Archer's increased stress level is due to Porthos' illness, but Dr. Phlox suspects it has to do with Archer's repressed sexual tension.

Archer, Mayweather and T'Pol travel to an arctic world to apprehend a fugitive, when T'Pol is contacted by Vulcan High Command. The mission takes a dangerous turn when T'Pol begins having flashbacks that suggest the events she remembers about a former mission may not accurately relate to what happened.

In need of fuel, the Enterprise arrives at a Quonset mining colony for deuterium supplies. They discover that Klingons are forcing the colonists to give up all their deuterium. Archer and the rest of the crew work to train the colonists so they can fight back against the Klingons.

Noncorporeal aliens possess the bodies of the Enterprise crew.