Captain Archer and temporal agent Daniels have been stranded in the 31st century. In a library they investigate the damage to the time line and try to find way a to get Archer back in his own century. Meanwhile Silik the Suliban leader is trying his utmost to find the whereabouts of Archer and he is willing to go far for the answer. But the crew of Enterprise has plans of their own. Trip finds a way to use the com system and is able to speak with Reed. Together they try to contact other crew members and make plans to purge Enterprise of the Sulibans.

On the first anniversary of her assignment to Enterprise, T'Pol tells Archer and Trip about the first contact between humans and Vulcans, which involves three Vulcans becoming stranded in the town of Carbon Creek, Pennsylvania in 1957.

The safety of Enterprise rests on Reed's shoulders when the ship becomes trapped in a Romulan minefield and Romulan ships are closing in on them.

Enterprise seeks repairs from their encounters with the Romulans, where they stop at a desolate but idyllic repair station. But all is not what it seems when Mayweather is suddenly found dead.

After previously offending the Kreetassans, Enterprise attempts to make a better second impression, only to upset the alien race once again. A frustrated Captain Archer returns from the planet only to be further upset to find that his dog Porthos, has been affected by a pathogen native to the world. While Phlox works around the clock treating Porthos, Archer stands vigil in sickbay, experiencing first-hand the quirky everyday life of his Denobulan Doctor.

Enterprise visits a colony with a deuterium trading post. But the people seem to be pretty unwilling to trade. Are they hiding something?

T'Pol asks Captain Archer to join her on a mission to capture a Vulcan fugitive that escaped her years ago.

Upon returning from covertly observing a pre-warp culture, Lieutenant Reed realizes he lost his communicator somewhere on the planet. Archer and Reed return to recover the lost technology, only to find the natives found it first. Captured and interrogated, the crewmen find themselves doing even more damage to the culture, who have scanned the prisoners and know them to be of another race. Meanwhile, Tucker and Mayweather try to figure out how to activate the cloak on the Suliban cell ship so they can mount a discreet rescue.

T'Pol must save the ship after the crew becomes obsessed with trivialities during the approach to a black hole.

After Hoshi uses the transporter to avoid running into a storm, she starts to feel very strange.

While Trip is repairing a stasis pod at a Retellian cargo ship and the woman inside, heir apparent to the throne of Krios, wakes up, the ship makes a hasty departure. Trip must make a plan to escape.

After receiving a warning about a radioactive storm approaching Enterprise, the crew is forced to take shelter in the ship's catwalk.

Trip's shuttlepod is shot down by a hostile race and is forced to land on a deserted moon. There he must team up with the alien who shot him down in order to find a way back to Enterprise.

T'Pol is diagnosed with a possibly fatal neurological disease as a result of a mind meld. Meanwhile, one of Phlox's wives visits Enterprise and becomes very interested in Trip.

Captain Archer is asked to negotiate between the Andorians and Vulcans who are fighting over a small planet.

Enterprise discovers a pod with the body of a human that seems to be wanted by both Sulibans and Tholians.

Archer and Trip are accused of smuggling and sent to the penal colony Canamar. While Enterprise manages to negotiate their release, a mutiny breaks out on the prison ship.

Enterprise is held captive by non-corporeal beings who claim to be explorers.

After Enterprise lends aid to a group of accused rebels, Captain Archer faces a tribunal and charges of conspiring against the Klingon Empire.

Mayweather temporarily leaves Enterprise to visit the cargo ship Horizon, where he was born and raised. Meanwhile, the Enterprise crew observes an unusual planetary event.

At Dr. Phlox's request, Enterprise attempts to retrieve 3 Denobulan scientists from the planet Xantoras, where the Goverment has ordered all off-worlders to evacuate within 3 days. Tucker, Reed, and Mayweather navigate a series of labyrinthine underground caves in search of the scientists. Meanwhile, Enterprise lends assistance to a damaged ship fleeing the planet. Doctor Phlox faces an ethical dilemma when one of the refugees of the ship refuses life-saving treatment. The patient, an Antaran, holds a grudge against Phlox stemming from a war between their races that ended 300 years ago and would rather die than be treated by a Denobulan. Phlox defies Archer's direct order to force treatment because it goes against the Deobulan code to yield to "the will of the patient."

Enterprise encounters a hyper-giant star. While there, they make first contact with the Vissians, a technologically sophisticated race with three genders. While making quick friends, and eagerly learning about the advanced technology, Trip gets curious about the Vissians third gender, known as the Cogenitor, who is crucial in the Vissian reproductive process. Against the wishes of the Vissians, Trip befriends the Cogenitor and encourages it to defy its cultural boundaries, which the Vissians are made aware of, and are angered by.

An Arctic research team makes a startling find: cybernetic creatures - Borg - buried in the ice. When the revived aliens seize control of a spacecraft, it's up to Archer to keep them from contacting the Collective and threatening Earth.

After his close friend and colleague A.G. Robinson is killed in a mountain climbing accident, Captain Archer tells T'Pol about the Warp 2 test flight almost ten years earlier.

After exploring an uninhabited planet, Captain Archer is taken prisoner by a Tellarite bounty hunter who was hired by the Klingons to return Archer to Qo'noS.

An alien probe launches a devastating attack on Earth. Archer, still being hunted by the Klingons, brings the Enterprise back home to investigate.