In the nine decades following Zefram Cochrane's visionary warp flight in space and the First Contact that followed, the human race has been slowly guided by the Vulcans toward developing the Warp Five engine. Mankind is at last able to explore the virgin depths of space with a revolutionary new starship, the Enterprise NX-01, under the command of Captain Jonathan Archer. Plans to launch Enterprise are moved up when a Klingon courier is shot down by unknown assailants and crash-lands in Broken Bow, Oklahoma. Feeling that the Vulcans have been condescending toward mankind for years, Archer insists it's the humans' responsibility to return the injured Klingon to his homeworld alive. Archer is fully backed by Starfleet Command, and the Vulcans' objections fall upon deaf ears.

In the nine decades following Zefram Cochrane's visionary warp flight in space and the First Contact that followed, the human race has been slowly guided by the Vulcans toward developing the Warp Five engine. Mankind is at last able to explore the virgin depths of space with a revolutionary new starship, the Enterprise NX-01, under the command of Captain Jonathan Archer. Plans to launch Enterprise are moved up when a Klingon courier is shot down by unknown assailants and crash-lands in Broken Bow, Oklahoma. Feeling that the Vulcans have been condescending toward mankind for years, Archer insists it's the humans' responsibility to return the injured Klingon to his homeworld alive. Archer is fully backed by Starfleet Command, and the Vulcans' objections fall upon deaf ears.

Two weeks into their first mission of deep space exploration, the Enterprise crew is still breaking in their ship and itching for first contact with another civilization. Captain Archer hears squeaking; Lt. Reed tests his weapons system on an asteroid field; Ensign Sato is trying to keep an alien slug alive; Commander Tucker tries the resequenced protein food; and Dr. Phlox is intrigued by human behavior. Sub-commander T'Pol detects a ship floating immobile in interstellar space, so Captain Archer decides to try to make contact with it. Getting no response, the crew takes a closer look at the alien vessel and sees evidence of weapons fire, and bio-scans reveal lifeforms with very low cellular activity. Over T'Pol's protestations, Archer orders Reed to prep a shuttle, and asks an apprehensive Hoshi to come along.

The infinite blackness of space is interrupted for the Enterprise crew by the discovery of a beautiful new world - a natural Eden of unexplored mountains, rivers, wildflower fields and forests. Dismissing T'Pol's cautious advice to conduct scans and tests from orbit before commencing any surface exploration, Captain Archer orders an away team and shuttlepod prepped. Joining Archer on the team are Crewmen Cutler, an entomologist, and Crewman Novakovich, a botanist, along with Commander Tucker, Ensign Mayweather, and T'Pol. Even Porthos, Archer's dog, comes along for the ride. The landing party takes in the fresh air of the virgin world before splitting up to pursue their specialties and enjoying a day of exploration amidst uncountable new species of exotic plant and animal life. At day's end, T'Pol, Cutler and Novakovich request permission to stay overnight to study nocturnal life, while Tucker and Mayweather ask to stay for the sheer fun of camping under the stars.

When Trip is dispatched to assist an alien ship with its power source problems, he is delighted to have a friendly encounter with one of the ship's female engineers. But after discovering that their special moment has resulted in his becoming pregnant, he realizes he's had an unwitting experience with alien sex. Archer and his crew must then try and return the rapidly growing alien baby to its mother.

Over 75 years ago the spaceship Conestoga left Earth on a nine-year one-way mission to establish the first human colony outside the solar system, called Terra Nova. The colony thrived on their beautiful new planet, and was such a success the Space Agency on Earth decided to send another vessel. The colonists protested and angry messages were traded, then one day all transmissions from Terra Nova ceased. Decades later the Warp 5-capable Enterprise NX-01 is dispatched to find out what happened to that lost colony.

As Enterprise warps through the depths of space, Captain Archer decides to take the opportunity to visit a nearby ancient Vulcan monastery called P'Jem, a sanctuary for meditation and "Kolinahr", or purging of emotion. T'Pol briefs Archer and Commander Tucker on the proper protocols for such a visit, and the three of them take a shuttlepod to the 3000-year-old temple. Something seems amiss as the trio enters, finding it suspiciously unoccupied with damage to the building and the artifacts. A Vulcan Elder informs them they are interrupting Kolinahr and must leave, but Archer notices a reflection in an urn of a strange alien hiding with a weapon. He and Tucker rush the intruder, but then find themselves surrounded and captured by a group of militaristic blue-skinned aliens.

The Enterprise crew is thrilled to encounter the biggest comet humans have ever seen, one that's 82.6 kilometers in diameter with a spectacular tail. Learning the comet contains large quantities of eisilium, an extremely rare mineral, Captain Archer dispatches Lt. Reed and Ensign Mayweather to take a little "comet-walk" with a drilling rig to collect samples. As they prepare for their mission, a Vulcan starship, the Ti'Mur, approaches unannounced. Archer hails the ship, and its captain, Vanik, informs him they are not there to investigate the comet, but rather to investigate Enterprise's interest in the comet. Although irked, Archer gracefully invites Vanik to stay and watch, but then he pulls T'Pol aside to find out what they're "really" doing here. T'Pol has no answers.

Excitement is brewing onboard Enterprise as the starship enters orbit of a Minshara-class planet with 500 million lifeforms. Visual and acoustic scans reveal a pre-industrial society called the Akaali. Over T'Pol's protestations of protocol, Captain Archer decides the crew should explore the civilization first-hand, rather than use probes. But the mission becomes more critical when neutrino emissions are detected on the surface, indicating an antimatter reactor on a world that doesn't even have indoor plumbing. So Archer sends himself, Ensign Sato, Commander Tucker and T'Pol down to the planet disguised as Akaali to investigate.

Sent by Admiral Forrest to respond to an automated distress call, Enterprise intercepts the Earth cargo freighter Fortunate and finds it badly damaged and not responding to hails. Captain Archer leads an away team to board the vessel, and they are greeted by the freighter's acting commander, first officer Matthew Ryan. Ryan informs Archer that the Fortunate was attacked by Nausicaan pirates, who have been harassing freighters in the sector for years, including the one Ensign Mayweather grew up on. Claiming the distress call was a mistake, Ryan resists Archer's overtures of help, but Dr. Phlox insists on tending to the injured captain. Once Phlox determines that Captain Keene will need two or three days of treatment, Archer talks Ryan into letting Enterprise engineers come aboard the Fortunate to upgrade its defenses. This forces Ryan and another crewman named Shaw to take special precautions to hide their secret - they have a Nausicaan prisoner on board whom they are torturing for information.

Enterprise navigates into a stellar nursery hoping to make contact with some of the alien vessels detected among the colorful gases and protostars. Finding a transport vessel escorting a group of alien pilgrims to the "Great Plume of Agosoria", a protostar which emits an epic burst of energy every 11 years, Captain Archer decides to caravan with the pilgrimage ship, and invites the group for a social dinner onboard Enterprise. Relations fare well among the starship crew and the pilgrims culminating with Commander Trip Tucker giving a guided tour of the Enterprise engineering bay. As the group listens attentively to Trip's oversimplified explanation of the warp engines, one pilgrim silently slips behind a bulkhead unnoticed. He opens a panel and dislocates his limb in order to disconnect a conduit within - he is a Suliban. After the disguised invader rejoins the group, the entire ship is suddenly rocked by a powerful plasma storm within the stellar nursery. Unsuccessfully attempting to steer clear of the storm, Enterprise is repeatedly hit with plasma lighting, severely damaging the warp manifold and starting a disastrous antimatter cascade traveling towards the reactor. Instead of completely destroying the ship, though, the cascade is suddenly stopped dead at the very console the Suliban tampered with moments before.

The Enterprise crew is in the process of deploying the second in a series of subspace amplifiers that will allow better communications with home, when an unidentified ship drops out of warp. Captain Archer hails the vessel, but it ominously refuses to respond and just warps away. T'Pol dismisses the "silent treatment" by stating that not every species has motives that can be understood in human terms. So Archer turns his attention to a more pressing concern - doing something special for Lt. Malcolm Reed's upcoming birthday. Archer breaks in the new subspace amplifiers by calling Reed's parents on Earth in hopes of learning his favorite food. He's a bit surprised to learn during the awkward conversation that the lieutenant's own parents don't know what he likes to eat. So the captain gives a reluctant Ensign Hoshi Sato the "mission" of discovering this bit of information about Reed in time for his birthday.

Now that the Enterprise crew is communicating regularly with Earth, Hoshi observes that Dr. Phlox is getting more letters from home than anyone else. Phlox has been corresponding with a human medical colleague named Dr. Lucas, who is now serving on Phlox's home planet Denobula. In his letters Phlox shares his observations of human behavior during their first deep space venture, and he mentions his growing relationship with Ensign Cutler, whom Phlox is mentoring to be a part-time medic and who he suspects is romantically interested in him. Phlox is called on to treat two alien astronauts rescued from a disabled pre-warp craft. The astronauts reveal they are from a planet called Valakis, and have been traveling in space for over a year searching for technology to develop a cure for an epidemic that is slowly hugging their people. The Valakians appeal to Captain Archer to allow Phlox to help them, and without objection from T'Pol, Archer agrees and sets course for their world.

When Enterprise comes across a wounded Klingon vessel, T'Pol, Hoshi and Reed take a shuttlepod down to investigate. There they are ambushed by a hostile female Klingon who hijacks the shuttlepod, leaving the Enterprise crewmembers dangerously stranded aboard the Klingon vessel. Now it's up to Archer to take the Klingon under guard and enlist her help in rescuing his crew.

Archer and the crew are disappointed to discover that T'Pol has been ordered by the Vulcan High Command to leave Enterprise -and equally frustrated at her seeming indifference to leaving their ranks. T'Pol's last mission as a Starfleet officer, however, proves eventful when she and Archer are kidnapped by a militant faction on an alien planet. However, aid comes to them in the form of the Andorians: their leader, Shran, still owes Archer a debt (from the events of "The Andorian Incident"). It turns out the Vulcans are covertly backing the ruling faction on the planet, while the Andorians are aiding the freedom fighters. With the help of the Andorians, Malcolm and Trip rescue Archer and T'Pol over the objections of the local Vulcan ship, and Shran considers his debt to Archer repaid.

Commander Tucker and Lt. Reed have been on a mission to test the targeting scanners on Shuttlepod 1, requiring them to fly the craft at least 20,000 kilometers from Enterprise. During their trials they experienced an unusual jolt that disabled their sensor array and com system, forcing them to return early to the asteroid field where Enterprise has been engaged in a mapping project. Upon arriving at the rendezvous point, the two men are shocked to find a field of debris on an asteroid's surface, including a hull fragment that is unmistakably a piece of Enterprise.

En route to exploring the Arachnid Nebula, the crew of Enterprise NX-01 is hailed by a civilian Vulcan ship. The ship's captain, Tavin, reveals that his vessel is in need of repairs. Archer offers to help, provided the Vulcans don't mind tagging along for the exploration of the nebula. While the Vulcan engineer, Kov, and Commander Tucker work together to repair the ship, Archer and T'Pol host Tavin and one of his crew, Tolaris, for dinner. Over the course of the meal, Archer and T'Pol are shocked at the emotionally pleasant and open nature of their guests. Tavin explains that he and his crew are referred to as "V'tosh ka'tur" ("Vulcans without logic") by the Vulcan elders. He clarifies that they are on a pilgrimage to explore and incorporate their emotions, to find a balance between emotion and logic.

While exploring an uncharted planet, Enterprise crew members encounter a group of aliens who are hunting down indigenous creatures for recreation. During their exploration, Archer is mesmerized by visions of a woman desperately attempting to communicate with him. The woman's ethereal distress signal informs Archer that she and others like her are actually the prey of the alien hunters. Heeding her call, Archer levels the playing field against the alien hunters.

When the entire crew is rendered unconscious, a quartet of large-eared, bickering thieves invades Enterprise. These plunderers, the Ferengi, are determined to make off with everything that's not bolted down. Meanwhile, Trip awakens after a long stint in the decon chamber and senses that something's not right on the ship. After spotting the thieves in action, Trip does his best to stay hidden and formulate a plan.

Archer, Tucker and T'Pol partake in a spicy dinner with an exotic alien trader named D'Marr, discussing with him their needs for raw materials to patch up Enterprise. In exchange for a few kilograms of an Earth beverage called "coffee", D'Marr reveals the location of an old vessel that crash-landed years ago on a nearby planet, a shipwreck that no one else has salvaged because it's "haunted". The crew locates the derelict ship and goes to take a look, joking that maybe they should calibrate their sensors for ghosts. Breaking into the spooky wreckage, Tucker and T'Pol look for engineering while Archer and Mayweather try to find clues as to what happened to the ship. As Tucker uncovers dilithium crystals he says are in perfect shape, T'Pol sees the reflection of a humanoid figure, who disappears immediately when she turns. T'Pol reports that someone is there, despite the fact that scanners show no bio-signs. She and Tucker spot the figure again and follow him, but find themselves at a dead end. Tucker uses his phase-pistol to cut open the bulkhead, and they discover a lush airponics bay behind it - hidden to their sensors by a dampening field. Exploring the oasis, Tucker is stopped dead in his tracks by an attractive humanoid woman, who immediately rushes away. Tucker and T'Pol chase her into a cargo bay, where they come face to face with 18 aliens pointing weapons at them.

While exploring a planet, Archer and Mayweather enter a "military zone" and are detained in an internment prison by an alien race called Tandarans, who are at war with the Suliban. While the Enterprise crew's previous encounters with the Suliban have been disastrous, Archer and Mayweather find themselves sharing a cell with some Suliban detainees who they believe may be wrongly imprisoned.

A strange, symbiotic alien creature boards the Enterprise capturing a few of the crew members, including Archer and Trip, and cocoons them in its web feeding off their bodies to survive. With the captured crewmembers' lives in jeopardy, Hoshi, under T'Pol's command, faces her biggest challenge by trying to find a way to communicate with the lifeform in order to return it to its home planet.

After ten months without a break, T'Pol notes efficiency onboard Enterprise is down three percent, and suggests a shore leave on the nearby tropical planet of Risa. Archer and Trip agree wholeheartedly and lay in a course to the exotic paradise. However, en route Archer receives a transmission from Admiral Forrest, informing him of a Vulcan Ambassador in need of immediate extradition from the nearby planet of Mazar. The matter is of some urgency, and with the closest Vulcan vessel over a week away Enterprise is to retrieve the Ambassador and deliver her to the Vulcan ship Sh'Raan at a rendezvous point in three days time.

After a brief detour, Enterprise and its crew are back on their way to famed pleasure planet Risa. Everyone is eagerly anticipating a long overdue shore leave ... until they pick up a distress call from an unidentified vessel, and vacation is once again delayed. After figuring out that the vessel's warp injectors are simply clogged with plasma residue, Trip gets to work repairing the engines while Archer enjoys a visit with the ship's captain, a ruggedly charismatic alien named Zobral. Hailing from a nearby desert planet, Zobral invites Archer and Trip to his home for a dinner in their honor. Though Archer is reluctant to accept the invitation since it means delaying shore leave yet again, he eventually relents, charmed by Zobral's persistence. Later, Archer is surprised to find Trip unenthusiastic about the invitation. The chief engineer confesses that he's hated desert environments ever since their harsh survival training in the Australian outback. Archer, however, manages to convince Trip to come along.

Finally arriving at planet Risa, the weary Enterprise crew eagerly embarks on a long overdue shore leave on the tropical paradise for two days and two nights. As some of the crew needs to stay onboard and run the ship, Captain Jonathan Archer institutes the drawing of lots to determine who can take leave. Winning a vacation himself, Archer feels both guilty for taking a break and also suffers from premature separation anxiety for leaving the Enterprise. With the comfort of T'Pol remaining onboard, the Captain is finally able to board the shuttlepod along with Trip, Reed, Mayweather and Hoshi. Everyone seems to have quite varied agendas for their short time on the planet: Mayweather plans to do some rock climbing on a cliff that changes pitch while you climb it; both Trip and Reed plan to meet some of the female aliens and ... broaden their cultural horizons; Hoshi feels she has had to rely on the Universal Translator far too much, and therefore plans to put her linguistic skills to the test with the various alien languages she hopes to encounter; while Archer booked a small cabin overlooking the ocean, and simply plans to relax with a good book and Porthos. Once the shuttlepod lands on Risa, the eager crewmates all go their separate ways.

Eager to visit the deep-space colony of a race called the Paraagans, Captain Archer leads an away team toward the surface of an alien planet. While piloting the shuttlepod into the atmosphere, Reed proceeds cautiously as he follows the Paraagan landing protocols precisely, a necessity due to the high concentration of the volatile gas tetrazine at a certain altitude. He closes the shuttlepod's plasma vents as instructed (exhaust plasma being the only thing hot enough to ignite the tetrazine), but just then the shuttlepod is rocked by a deafening explosion, and a massive shockwave scorches the planet beneath them. After getting back to Enterprise safely, the distraught team learns the colony of 3600 people has been obliterated, and tries to figure out what happened. Reed is absolutely certain both plasma ducts were closed without malfunction, but Archer orders an investigation while he braces himself to report the incident to Admiral Forrest. While the crew continues its analysis and Archer deals with intense feelings of guilt, Forrest convenes an emergency meeting of the Command Council. He later informs Archer that Enterprise is to return home, and a Vulcan ship will rendezvous with them in three days to pick up T'Pol and Dr. Phlox.