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.

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

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

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

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

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.

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.

Enterprise answers a distress signal from a stranded Vulcan ship, only when arriving they find the ship completely desolate, wrecked - and filled with Vulcan zombies.

His memory crippled, Archer awakens years in the future, after the Xindi have reduced Earth to a cinder and the remnants of humanity have settled on a distant planet. Now, Archer learns that he may be the key to undoing this tragedy.

With Reed and Hayes fighting over a training program and Trip seemingly making T'Pol jealous, Enterprise discovers a dying alien in a pod with technology similar to the Spheres.

Captain Archer has been returned to Enterprise by the Xindi council awaiting a hearing. But after a heavy attack by the Reptilians, Enterprise is stranded without a functional warp drive. They meet another ship in trouble because of space anomalies. The ship's captain isn't willing to trade in their warp coil and Archer must make a tough decision. Meanwhile T'Pol is having some strange sensations and can't control her emotions.

The Augments are on their way to Cold Station 12, where Augments embryos are kept.

The Augments have yet again escaped. While Dr. Soong wants to hide the embryos, Malik has an entirely different and way more cruel plan.

T'Pol and Archer confront the Syrrannites and meet T'Pau who denies the embassy bombing. Archer, who has Surak's essence, is asked to help. V'Las threatens Enterprise to make sure an attack on the Syrrannites isn't witnessed.

Dr. Emory Erickson comes aboard to supposedly conduct tests for subquantum transportation. However, he seems to have a different agenda.

While Enterprise is visiting Earth, Phlox is abducted by the Klingons and forced to research a cure for a virus destined to wipe out the race. Reed is tapped by a secret agency and ordered to betray Archer. Trip transfers to the Columbia.

Set in the dark and oppressive Mirror Universe, Commander Archer leads a mutiny in a bold attempt to seize control of an advanced starship - a vessel from the future that may be the key to saving the Terran Empire.

While attending a conference on a proposed interplanetary alliance, Trip and T'Pol find out from a dying woman that they have a baby. Investigation shows the woman was a member of the xenophobic organization Terra Prime.