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.
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.
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.
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.
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.
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.
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.
After an away mission, Lieutenant Reed discovers that his communicator was lost on a pre-warp planet; he and Captain Archer are then captured trying to retrieve it.
Enterprise charts a course through a trinary star system to investigate a black hole, and the crew find themselves suffering from a condition similar to OCD.
After her first trip through the transporter, Ensign Sato finds herself becoming incorporeal, with the crew believing she has perished.
Trip boards an alien cargo vessel to help repair a stasis pod, which holds a beautiful woman in suspended animation. When the woman accidentally wakes up, she reveals she's not a passenger, but a prisoner.
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.
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 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.
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.
Incorporeal aliens attempt to take over Enterprise.
Captain Archer is arrested and imprisoned by the Klingons for allegedly conspiring against the Empire.
After the death of his father, Ensign Mayweather visits his family on their cargo ship and begins to reconsider his place aboard Enterprise.
Due to the demands of a militant faction, Enterprise is asked to retrieve Denobulan geologists from an alien cave. Dr. Phlox must treat a patient with racist views against his people.
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.
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.
Upon the death of a close friend, Captain Archer tells Sub-Commander T'Pol about his early career as an experimental warp engine pilot.
A Tellarite captures Captain Archer in order to collect a reward from the Klingons who have been searching for him since the events of "Judgment".
After an alien attack on Earth, Enterprise is refitted before being sent into the Delphic Expanse. Sub-Commander T'Pol resigns her commission with the Vulcan High Command, and Commander Tucker is troubled by the death of his sister.