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- Ensign Vorik's attempt to make B'Elanna his mate during Pon farr biochemically destabilizes B'Elanna, heightening her own aggressive emotions towards taking a mate.
- Aboard the Delta Flyer, Janeway leads Tuvok, Paris and the Doctor on a rescue mission to retrieve Seven from the Borg Queen. whose treatment of Seven is markedly atypical.
- 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.
- After an attack by Osaarian pirates, Enterprise follows them to a mysterious sphere.
- 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.
- 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.
- 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.
- Dr. Emory Erickson comes aboard to supposedly conduct tests for subquantum transportation. However, he seems to have a different agenda.
- 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.
- 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.
- 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, Reed and Sato are transformed into aliens while visiting a planet.
- 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.
- 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 answers a distress signal from a stranded Vulcan ship, only when arriving they find the ship completely desolate, wrecked - and filled with Vulcan zombies.
- 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 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.
- 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.
- Archer decides to make a fast-growing clone of Trip to help save his life while Enterprise is stranded in a dangerous field with nucleonic particles.
- 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.
- Archer sends an away team to a habitable, luscious planet for observation. But when a storm occurs, the team begins to experience paranoid delusions.
- 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."
- After receiving a warning about a radioactive storm approaching Enterprise, the crew is forced to take shelter in the ship's catwalk.
- 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.
- An alien probe launches a devastating attack on Earth. Archer, still being hunted by the Klingons, brings the Enterprise back home to investigate.
- Enterprise follows a lead and discovers a Xindi lab that refines Kemocite, the key ingredient in the weapon being built to destroy Earth. An away team of Archer, Reed and Hayes confront the lead researcher, Gralik Durr, who was employed by Degra to refine the Kemocite but was never told what it would be used for. When Gralik realizes it was his research that contributed to the 7 million deaths on Earth, he agrees to help Archer prevent further loss of life. Meanwhile, on Enterprise, Phlox and Tucker study the weapon they seized from the Xindi and find an organic component, a life-form serving as the rifle's power cell. Despite T'Pol's objection, Tucker tests the weapon.
- Enterprise has been in the Delphic Expanse for six weeks and have yet to get any intel about the Xindi. Strange anomalies affect the ship, sending cargo flying violently through the bays, pockets of atmosphere losing gravity and other incidents defying the known laws of physics. T'Pol helps Trip's insomnia with an intimate Vulcan therapy. Archer and Trip find another race of Xindi imprisoned in a mine.
- 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.
- 2001–200545mTV-PG6.6 (1.8K)TV EpisodeThe 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.
- Capt. Janeway recalls her ancestor, Shannon O'Donnell, with great reverence, but historical records don't back up the family story.
- Janeway tries to make an alliance with a Kazon sect for their own protection and so they can continue their journey through the Delta Quadrant.
- Ens. Kim and Lt. Tuvok become rivals in love over what at first seems to be a holodeck character.
- Voyager receives a former crewman, deceased, resurrected, genetically altered, unrecognizable, and glad to be "home." Meanwhile, looking after the Borg children exasperates Seven of Nine.
- A brutal experience aboard a shuttle puts B'Elanna in touch with the Klingon afterlife, where the Barge of the Dead steers her towards Klingon hell along with her mother.
- On her deathbed, Kes relives her life, jumping backwards in spurts of time towards birth, gaining knowledge as to why as she goes.
- The Voyager crew discovers what seems to be a wormhole leading to the Alpha Quadrant and home. Images of Earth and letters from home elates the crew of Voyager. Seven, and others, however, are skeptical of this seeming deliverance.
- An encounter with a peculiar nebula suddenly leaves Chakotay brain dead and unconscious. The crew is left with a mysterious but powerful force of energy onboard that can take over the minds of the crew members.
- The Caretaker's remains resonate, which might well mean that its mate is nearby. The trail leads to a space colony of Ocampa with psychokinetic powers.
- After aliens raid Voyager, Janeway discovers her Leonardo holodeck character living independently at a trading post under the patronage of a shameless "prince" of thieves.
- Needy alien refugees, who look upon Voyager's generosity as stingy, put Torres and Paris in a life-threatening situation during a crossroads in their relationship.
- A schism duplicates everything in Voyager; except the antimatter, which both ships share. As one ship rips apart, the other comes under attack from organ-harvesting Vidiians.
- Critically low on energy, Voyager limps to a hellish Y-class "Demon" planet for much needed deuterium. Harry and Tom beam down and make accidental contact with a gooey life form.
- An encounter with aliens in a subspace corridor leads Voyager to take refuge on a radioactive planet with remnants of its civilization tucked underground in stasis chambers.
- Tom's sudden entry in an alien spacecraft race throws a wrench into B'Elanna's labored plans for a romantic holodeck getaway for two, threatening their relationship.
- Voyager discovers another Federation starship in the Delta Quadrant, one that's had a rougher time getting home, on its last legs, and harboring a dark secret.
- While trying to run down the Equinox and retrieve its captain, Chakotay fears Janeway becoming equally as unethical and corrupt, challenging his loyalty.
- Tuvok plays detective when Paris is wrongfully convicted by an alien race of murder.
- In an attempt to develop a cure for the Phage, a Vidiian doctor captures Torres and splits her into her 2 halves, one human - the other, Klingon.
- Capt. Janeway falls for an Irish barman character she modifies within Tom's holodeck Irish village recreational getaway for the crew called Fair Haven.