Archer, Trip and T'Pol are captured by the Andorians at a Vulcan monastery on P'Jem. They believe that the monastery is being used to spy on Andoria.

Enterprise has a group of aliens watching a stellar phenomenon on board. When the ship is miraculously saved from blowing up, crewman Daniels has an important message for Archer.

Phlox is asked to save the Valakians from annihilation by disease. However, he discovers something unusual about the Menk, another humanoid race on the planet.

Enterprise tries to rescue a Klingon ship from sinking into a gas giant.

When Enterprise encounters a ship of Vulcan pilgrims, T'Pol is convinced by one of them to perform a Vulcan mind meld.

Lieutenant Reed discovers a rogue planet, which has broken out of orbit and therefore is devoid of any light. Life is still possible in some places because heat is bubbling up from under the surface, but T'Pol doesn't detect any humanoid life. Further scans however give a strange energy reading which seems to be coming from a ship on the surface. After the crew has landed, they encounter the Eska. The Eska come from another planet and they say they are hunting for the drayjin, an animal considered a delicacy. When captain Jonathan Archer tries to sleep on the planet, he hears a voice calling him by his name. A human female is wandering in the forest. Somehow he seems to know her.

Almost the entire crew is left unconscious when four Ferengi pirates raid Enterprise. A still conscious Trip is the only one who can get rid of them.

The crew of Enterprise searches for a seemingly abandoned ship on a desert planet.

A fibrous, web-like alien creature comes aboard the ship and several of the crew becomes entangled in it including Archer and Trip, and it seems Hoshi is the only one who can try to communicate with the creature.

Enterprise is planning a trip to the relaxation planet Risa, when it gets an urgent request from the Vulcan High Command. They must pick up ambassador V'Lar who has fallen in disgrace. Apparently she misused her position during negotiations on the planet Mazar and has been evicted. After Enterprise picked up V'Lar and is on its way for a meeting with the Vulcan warship Sh'Ran, suddenly a Mazarite ship appears. They want V'Lar for further interrogating. When captain Archer wants to discuss it first with Starfleet Command, they open fire.

The members of the Enterprise crew are faced with various misadventures and challenges while taking a two day break from their duties on the planet of Risa.

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 asks Captain Archer to join her on a mission to capture a Vulcan fugitive that escaped her years ago.

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

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

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.

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 an attack by Osaarian pirates, Enterprise follows them to a mysterious sphere.

Enterprise helps an alien woman, Rajiin, seeking to escape her life as a sex slave. Once on board she uses her alien abilities to gather biometric data about humans and is recaptured by her employers, the Xindi council.

Hoshi Sato is contacted by a 400-year-old telepathic alien exiled on planet in the Expanse, shunned by his society because of his abilities. The alien offers to use his powers to help Enterprise find the Xindi and the weapon they are building, but only if Hoshi will stay with him while he works. She agrees to stay behind, while Enterprise confirms the Expanse has a second Sphere and is on its way to investigate.

Archer and the Xindi Degra are in a shuttle. With Degra suffering from memory loss, Archer tells him they escaped together from a prison and that the Insectoids took power after destroying Earth.

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.

While in command of Enterprise because the entire crew is in a coma, Dr. Phlox starts hearing some strange sounds.

After a bombing destroyed the Earth embassy on Vulcan, a group known as the Syrrannites are suspected. T'Pol receives a map from her Syrrannite mother, leading into a dangerous desert, the Forge.

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.

Enterprise escorts Tellarites to peace talks with Andorians. While transporting they rescue Andorians and say the Tellarites attacked them. Enterprise is soon attacked by an Andorian ship, and Archer must prove who is responsible.

Captain Archer must convince Vulcans, Tellarites and Andorians to unite to find the Romulan ship.

Enterprise finds out the marauder was piloted telepathically by an Aenar, a subspecies from Andoria.

While Enterprise tries to bring Trip on board to reverse the malicious Klingon modifications, Phlox and Antaak find a cure for the virus that will not please General K'Vagh.

The men of Enterprise fall under the seductive control of three Orion women. Trip is the only male member of the crew not to succumb to the women.

Paxton threatens to destroy Starfleet Headquarters if all aliens don't leave Earth. Enterprise must shut down the verteron array on Mars, but it is extremely well defended.