Silik and his Suliban soldiers board Enterprise to search the ship for Captain Archer, who T'Pol insists disappeared when he left to give himself up. Meanwhile, Archer is stuck in the 31st century with Daniels, trying to determine why his removal from the 22nd century led to the devastation they are witnessing. Daniels is stunned to discover that a monument commemorating an organization called the "Federation" was never built. The two find a dilapidated old library and begin searching for answers there. On Enterprise, the Suliban re-take the data disks stolen from them earlier showing they were the ones responsible for the catastrophe on Paraagan II. They also detect a temporal signature on board which proves T'Pol was not lying after all about Archer, so rather than killing the crew, Silik confines them to quarters and commandeers the ship. Meanwhile on Earth, Ambassador Soval is incensed that Enterprise has failed to follow instructions ending its mission, and tells Admiral Forrest he has no choice but to send the Vulcan ship D'kyr in pursuit.
Celebrating T'Pol's first full year with the Enterprise crew over dinner, Archer asks why her record states that she once took a five-day leave to visit an old Pennsylvania mining town called Carbon Creek. She claims Carbon Creek was the site of actual first contact between humans and Vulcans, long before the historical First Contact in 2063, and her second foremother (great-grandmother) was there. Trip Tucker scoffs at this, but then T'Pol offers to tell "the story".
Archer invites Reed to breakfast, hoping to become better acquainted with his armory officer. Reed, however, seems reluctant to discuss anything other than work. Just as Archer's getting frustrated, T'Pol alerts the captain that an uncharted system has been detected and one of the planets is Minshara-class. As Enterprise enters the planet's orbit, it is rocked by massive explosions, damaging sections of the ship and injuring several crewmembers, including Hoshi. Reed is able to discern that the ship has been hit by an alien orbital mine, which has attached itself to the hull. As the mine has the power to disable Enterprise, Reed suits up and heads out to defuse it. Uncertain that Reed will succeed in his task, Archer suggests an alternate plan to Trip - detach the section of hull plating surrounding the mine, allowing it to drift away. Trip notes that this will expose a good portion of the impulse manifold, but Archer tells him to get started on it anyway - the captain will consider the plan a last resort.
After the incident in the Romulan minefield, Enterprise is in need of repairs. Archer sends out a general distress call, and receives a jumbled response from a Tellarite freighter, containing the coordinates of a repair station. When the crew arrives at the station, it appears to be abandoned ... until one of the docking ports lights up and reconfigures itself to fit Enterprise. Still, there don't seem to be any lifeforms onboard. Once inside the station, Archer, T'Pol and Trip locate a sort of diagnostic center that contains holographic schematics of the ships, with the damaged sections clearly highlighted. Somehow, the station has managed to scan the ship and anticipate the crew's needs - the schematic even highlights Reed's recent leg injury. A computer voice addresses the trio, asking them to select a method of compensation for the repairs. Archer offers some warp plasma, and the station accepts, saying the repairs can be completed in less than 35 hours. Though he is wary of the automated nature of the station, Archer accepts the terms, and the station begins the repairs. In the station's recreation room, the trio is impressed by the amazing technology on display - a food replicator delivers both cold water and Trip's favorite fried catfish.
Having managed to offend the Kreetassans yet again while negotiating for a much-needed plasma injector, Archer returns to Enterprise frustrated. Things get even worse when he learns that Porthos picked up some kind of pathogen on the Kreetassan homeworld, and must be confined to sickbay. Unfortunately, Porthos' condition only worsens, and Dr. Phlox must prevent the beagle's auto-immune system from collapsing entirely. As Archer worries about the fate of his pet, T'Pol informs him that she has discovered the reason for the Kreetassans' anger. Apparently, Porthos urinated on one of the 300-year-old Alvera trees - which are considered cultural treasures - outside the Hall of Diplomacy. In order to receive the plasma injector for Enterprise, the captain will most likely have to perform several acts of contrition. This infuriates Archer even more - especially since he thinks the Kreetassans should have known there was a pathogen in their atmosphere that Porthos couldn't handle.
With Enterprise's deuterium reserves running low, Archer and the crew visit a small mining colony in hopes of replenishing their supply. The alien colonists, however, claim that they can't spare any deuterium, and ask Archer to return at the end of the season. Archer manages to negotiate, and eventually reaches an agreement with the colony's leader, Tessic - the deuterium in exchange for medical supplies, power cells and assistance in repairing the colony's extraction pumps. In a puzzling move, Tessic also insists that the pump be repaired within two days.
When T'Pol is assigned a secret mission by the Vulcan High Command, she asks Archer to accompany her. The captain is surprised by her request, but agrees - especially when T'Pol reveals that there is a personal side to the mission. Many years ago, T'Pol was sent to retrieve several rogue Vulcan operatives. She was able to apprehend all but one of them, a man known as Menos. Now, the Vulcans believe they have located Menos, and they want T'Pol to bring him in.
Upon returning from a research mission to a pre-warp alien planet, Reed discovers that his communicator is missing. After an extensive search, he realizes that he must have lost it somewhere on the planet. Hoshi manages to tap into the communicator's power signature and pinpoints its location near a tavern that Reed and the rest of the team visited. Archer knows that the crew must retrieve their technology or risk contaminating the planet's pre-warp society, so Archer and Reed return to the planet, hiding their shuttlepod in the woods. As they enter the tavern, a group of soldiers eyes them suspiciously. Using his scanner, Reed realizes that the communicator is located in another room of the tavern, but when he and Archer go to retrieve it, they are apprehended by the soldiers. The two men are taken to the tavern stockroom and questioned by Major Pell, who asks if the communicator is a weapon. Pell also seems to think Archer and Reed are connected to something called "the Alliance". When the men refuse to respond, Pell orders that they be taken to the military complex.
Enterprise has dropped to impulse in order to get a closer look at a black hole that's part of a trinary star system. As it will take them two days to get there, the crew has time for personal endeavors. Archer concentrates on writing a one-page preface for a biography of his father. He also assigns Trip the task of making some adjustments to the captain's chair, which is apparently rather uncomfortable. Reed hopes to work on a new security protocol, while Hoshi takes over cooking duties for an ailing Chef.
Hoshi and Trip are surveying some primitive alien ruins, taking pictures and discussing what might have happened to the people who used to inhabit the planet. Suddenly, Archer contacts them and asks them to return immediately to Enterprise - a storm is heading their way. As the duo prepares to board their shuttlepod, Archer contacts them again. The storm situation is more urgent than he predicted, and he needs to bring Trip and Hoshi up via the transporter, one at a time. Hoshi is apprehensive, and insists that Trip go first. Once he is safely onboard, she beams up.
The Enterprise crew has visitors - two Retellian cargo pilots, Firek Goff and Firek Plinn, need help repairing their life support systems. The pair explains that they have been hired to return a young woman to her homeworld. Because of their limited resources and the length of the trip, they are transporting her in stasis. A few days ago, her stasis pod began to malfunction. The crew cannot support a passenger out of stasis, so they need Trip's help repairing their systems. Firek Goff refuses Archer's offer to help them transport their passenger more quickly, but he does accept the captain's offer of a meal.
As Captain Archer prepares to lead a survey team to an uninhabited planet, Enterprise is suddenly hailed by a trio of aliens seeking refuge. The aliens warn Archer that a deadly neutronic wavefront is quickly approaching. After conferring with the crew, Archer surmises that everyone must take shelter somewhere protected in order to survive the storm's deadly radiation. Trip suggests that the one heavily-shielded place onboard that might suffice for the eight-day ordeal is the cramped quarters of the catwalk, the maintenance shaft that runs the length of each nacelle. Only one problem - the temperature in the catwalk can reach 300 degrees when the warp coils are online, so Trip will have to shut down the main reactor and set up a makeshift bridge in one of the catwalk compartments.
Trip is alone on a test mission aboard Shuttlepod One, trying out the latest autopilot upgrades. Suddenly, he is fired upon by an alien ship and must make an emergency landing on a nearby moon. It's nighttime, and Trip attempts to repair the transceiver in order to contact Enterprise. While he's working, he is suddenly attacked by a mysterious alien. Trip retreats into his shuttlepod, but quickly notices that the alien interloper has stolen his transceiver.
As Enterprise enters the orbit of Dekendi III, Dr. Phlox prepares to attend the Interspecies Medical Exchange conference. He's also looking forward to being reunited with one of his wives, Feezal, who will be helping Trip install a neutron microscope onboard. Phlox is pleased to see his wife, but the conference raises a troubling issue - Phlox is the only person onboard Enterprise who knows that T'Pol is suffering from Pa'nar Syndrome, an incurable Vulcan disease. He has been able keep the effects of the disease at bay, but he knows that T'Pol will soon need supplemental medications. Otherwise, she might die. The doctor sees the conference as the perfect opportunity to speak with Vulcan physicians, and learn if they have made any headway with the disease. However, he must keep T'Pol's identity a secret, as the High Command cannot learn of her condition.
The Andorians and the Vulcans are locked in battle over a small planet, situated on the frontier between their two systems. Both sides claim that it belongs to them - the Andorians refer to it as "Weytahm", while the Vulcans call it "Paan Mokar". Andorian Commander Shran has landed a force on the planet and occupied the settlement. Now, the Vulcans are calling for a cease fire and Shran wants Archer to help the two sides negotiate. Vulcan Ambassador Soval is reluctant to bring Archer in as mediator, but three Vulcans have been taken hostage, and Shran has made his position clear - he only trusts Archer.
When the Enterprise crew discovers a mysterious, futuristic vessel adrift in space, Captain Archer orders it brought onboard for further investigation. Inside the craft, the crew is shocked to find what is apparently a human body, charred beyond recognition. Trip and Reed take a closer look at the interior of the ship, and discover that it is much more spacious that it appears. They also discover a "black box" device within the depths of the ship and prepare to bring it up to Engineering for more research.
Upon leaving the Enolian homeworld, Archer and Trip are mistakenly identified as smugglers and arrested. The two men are placed on a prison transport headed for the penal colony known as Canamar. Among their fellow prisoners are the menacing Kuroda, a hulking Nausicaan and a young, talkative alien named Zoumas.
Enterprise encounters a large, otherworldly vessel unlike any the crew has seen before. They try to make contact with it, but to no avail. Suddenly, a large portal opens and the ship "swallows" Enterprise, rendering its weapons and engines useless. Luckily, life support is still operational. Archer, Trip and Reed take a shuttlepod into the cavernous ship for further exploration. Although there doesn't seem to be any immediate threat to Enterprise, Trip is suddenly attacked by a colorful wisp of smoke that seems to invade his body for a few seconds before releasing him. Back in Sickbay, Trip insists that he's fine. He explains that during his brief encounter with the alien wisp, he had an out-of-body experience and believed he was in Florida and visiting an old girlfriend.
On Narendra III, Archer stands before a Klingon court magistrate and a crowd of blood-thirsty Klingons. The captain is charged with conspiring against the Klingon Empire, and will stand trial. He is banished to his cell, where Dr. Phlox pays him a visit. The doctor, who is tending to Archer under the ruse that the captain is suffering from a mysterious illness, quietly lets Archer know that T'Pol and the rest of the crew are working on a way to free their captain. As Phlox leaves, Archer meets his Klingon advocate Kolos, who warns him not to speak during the tribunal.
Enterprise reverses course to investigate a geological phenomenon - a planet that's about to be covered with erupting volcanoes. The course change will take the ship near the E.C.S. Horizon, the cargo ship where Mayweather grew up. Mayweather requests a few days off to make a family visit - he hasn't been home in several years, and his father is ill. The ensign is somewhat nervous about seeing his family - his father didn't seem to approve of his decision to leave Horizon to join Starfleet. Ultimately, Mayweather's homecoming proves to be bittersweet - when he contacts his mother, Rianna, she reveals that his father died a few weeks ago.
Enterprise is asked to evacuate a group of Denobulan geologists from Xantoras, a world that has been taken over by a militant faction. The Denobulans are located in some underground caverns, so the rescue team - Mayweather, Trip and Reed - will have to traverse some treacherous rock formations in order to get them out. Meanwhile, another ship of off-worlders is headed away from Xantoras when their reactor casing is ruptured, flooding the ship with radiation. When the Xantoran officials refuse to let the ship land, Archer agrees to bring the evacuees onboard Enterprise for treatment. One of the evacuees is an Antaran named Hudak, who is horrified that Enterprise's doctor is Denobulan. Phlox explains to Archer that the Denobulans and Antarans have a troubled, bloody history between them - the two species have gone to war several times. Even though it's been three hundred years since the last conflict, much bad blood still exists between them.
Archer is thrilled to be within ten light years of a hypergiant star. As the crew prepares to study the phenomenon, they make first contact with another species - the Vissians, who are also in the area to study the hypergiant. After the Vissian captain, Drennik, explains that meeting new species is one of their primary goals, Archer invites him and his crew onboard Enterprise for dinner. Once there, Drennik and Archer hit it off, and Drennik invites Archer to join him when he takes the Vissian stratopod deep into the hypergiant the following day. Archer enthusiastically accepts the invitation. Meanwhile, other crewmembers are mingling with the Vissians. Reed hits it off with a female Vissian tactical officer, while Trip meets the Vissian chief engineer and his wife. Trip is intrigued by a third individual the couple has with them, a member of the species' third gender known as a "cogenitor". The cogenitor is a nameless individual who somehow makes pregnancies among Vissians possible - the engineer and his wife are trying to have a baby.
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.
Archer receives news that A.G. Robinson, his old rival in the early days of the NX test program, has died. During a shuttlepod mission, Archer reminisces to T'Pol about the time he and Robinson were pilots competing for the honor of being the first to break the Warp 2 barrier.
The crew of the Enterprise encounters Skalaar, a Tellarite who offers to give them a tour of a nearby planet. As it turns out, Skalaar is actually a bounty hunter who kidnaps Archer, planning to turn him over to the Klingons for a reward. The Klingons have apparently placed a substantial price on Archer's head since his escape from Rura Penthe. Archer tries to plead his case with Skalaar, but the Tellarite doesn't want to listen, and claims not to care if Archer is guilty of the crime he was imprisoned for. Archer soon learns that Skalaar plans on using the substantial reward money to buy back his cargo ship, the Tezra.
An alien race known as the Xindi launch an attack on Earth, causing great casualties and massive damage. As Enterprise heads back home, an unlikely source informs Archer about the Xindi and that their next attack will destroy Earth.