- Commander Chakotay is taken prisoner by the Kazon-Ogla after drifting into their space in a shuttlecraft while performing the pakra ceremony. He and a young Kazon boy named Kar make an escape from a Kazon carrier vessel to the moon Tarok. Afterward, Kar earns his name after killing Jal Razik and Chakotay completes the pakra ceremony on the USS Voyager. (VOY: "Initiations")
- A shuttle accident causes Harry Kim to be transported to an alternate timeline where he never served on board the USS Voyager. He is able to be transported back to his own reality with the help of an unknown alien and an alternate Tom Paris. (VOY: "Non Sequitur")
- Starfleet introduces a new style of phasers and tricorders in this year. (DS9: "The Way of the Warrior"; VOY: "Initiations")
- Convinced by a Changeling posing as General Martok that the Cardassian government had been infiltrated by the Founders, the Klingon Empire invades the Cardassian Union. However, the United Federation of Planets objects to this action, causing Chancellor Gowron to withdraw from the Khitomer Accords, ending their alliance. At the end of this year, the Changeling posing as General Martok convinces Gowron to take further aggressive action, causing the Klingon Empire to annex the Archanis sector from the Federation, thereby starting an open war between the two powers. (DS9: "The Way of the Warrior", "Broken Link")
- The Bajoran wormhole undergoes an inversion that occurs once every fifty years. (DS9: "The Visitor")
- Miles O'Brien and Julian Bashir are captured by a group of Jem'Hadar. Goran'Agar, their leader, orders Bashir to work on a cure for his men's addiction to ketracel-white. (DS9: "Hippocratic Oath")
- Commander Chakotay discovers the Sky Spirits living on a planet in the Delta Quadrant, who visited Earth some 45,000 years before and reveals himself to be a descendant of the Inheritors. (VOY: "Tattoo")
- Voyager encounters the Caretaker's mate, Suspiria and discovers that she is hostile. (VOY: "Cold Fire")
- The Antwerp Conference is bombed. An investigation reveals that the bomb was placed by a Changeling. Benjamin Sisko is temporarily reassigned to Earth to serve as Chief of Starfleet Security, in charge of preparing the Federation for a possible Dominion invasion. (DS9: "Homefront")
- Admiral Leyton stages a military coup by taking advantage of the current Changeling scare. The attempt is thwarted by Benjamin Sisko and Odo. Leyton resigns his commission, and Sisko and Odo return to Deep Space 9. (DS9: "Paradise Lost")
- The Kazon-Nistrim briefly steal transporter technology from Voyager. Chakotay is able to eliminate the Kazon's new-found technology and return to Voyager, but not before Seska informs him that she stole a sample of his DNA and impregnated herself with it. (VOY: "Maneuvers")
- The Korma Conference was scheduled to take place in this year, however the outpost hosting the conference was destroyed by a Klingon Bird-of-Prey that was later commandeered by Gul Dukat. (DS9: "Return to Grace")
- A member of the Q Continuum, Quinn, is released from his confinement in a comet by the crew of Voyager. After a brief trial, he relinquishes his powers so he can become Human and commit suicide. Q secures the poison used in the suicide. The event causes a civil war in the Continuum. (VOY: "Death Wish", "The Q and the Grey")
- Captain Kathryn Janeway attempts to form an alliance with various Kazon sects to bring a stop to their increasingly frequent attacks on Voyager. Unfortunately, the negotiations are put to a stop after the Trabe attempts to wipe out the Kazon delegates. (VOY: "Alliances")
- Voyager discovers a new type of dilithium which allows a shuttlecraft, piloted by Tom Paris, to achieve warp 10 flight. However, the effects of this type of transwarp are proved detrimental to humanoid DNA, and it is abandoned. (VOY: "Threshold")
- Michael Jonas begins secretly feeding the Kazon-Nistrim information about Voyager. Lieutenant Tuvok discovers the transmissions, but is unable to determine who sent them. In an effort to flush out the spy, Captain Janeway and Tuvok create a plan to have Tom Paris begin behaving like a malcontent to have a plausible reason for him to leave Voyager, be captured by Kazon forces, and extract information exposing the traitor. (VOY: "Investigations")
- A Cardassian missile reprogrammed by B'Elanna Torres is found by Voyager in the Delta Quadrant, set for a course to destroy a planet. The missile is destroyed by Torres before it strikes the planet. (VOY: "Dreadnought")
- Michael Jonas is revealed to be the traitor on Voyager supplying information to the Kazon. He is killed in a fight with Neelix. (VOY: "Investigations")
- Voyager encounters a plasma drift which somehow duplicates every single molecule on board the ship. Severe damage is inflicted to one Voyager, and Harry Kim dies after being blown out through a hull breach. Naomi Wildman is born to Samantha Wildman during the incident. The other Voyager is later attacked by Vidiians, but is able to send Kim along with the Wildman child, who survived on this vessel, to the damaged Voyager. The other Voyager then self-destructs. (VOY: "Deadlock")
- Violating the rules of Ferengi society, Quark's employees, led by Rom, form a union and go on strike. Quark secretly agrees to the unions demands in order to protect his brother, and the union is dissolved. Rom quits working for Quark and takes a position under Chief Miles O'Brien on Deep Space 9's engineering crew. (DS9: "Bar Association")
- A transporter accident combines Tuvok and Neelix into a single being, Tuvix. He is later separated into his two halves against his will by Captain Janeway. (VOY: "Tuvix")
- While escorting a medical convoy to Pentath III, Lieutenant Commander Worf accidentally destroys a Klingon civilian convoy. The Klingon Empire tries to have Worf extradited and charged for the deaths of the 441 civilians on board. Fortunately, it is revealed that the transport was empty and giving false readings to justify an armed conflict, and the casualty list was in fact a list of the victims of an accidental transport crash that occurred three months before this incident. (DS9: "Rules of Engagement")
- Captain Janeway and Commander Chakotay contract a virus from an insect bite, and are forced to be left behind on the planet which they were infected. Tuvok becomes Voyager's new commanding officer for six weeks until a cure is obtained from the Vidiians. (VOY: "Resolutions")
- After being convicted of espionage, Miles O'Brien is given the memories of a 20-year prison sentence on Argratha. (DS9: "Hard Time")
- Doctor Julian Bashir is able to prevent unborn children of the people living on Boranis III from contracting a plague sent by the Dominion as punishment for the rejection of their offer of membership. (DS9: "The Quickening")
- The USS Enterprise-E is launched from the San Francisco Fleet Yards on stardate 49827.5. (Star Trek: First Contact)
- Captain Benjamin Sisko takes the USS Defiant to the Founders' homeworld, hoping that the Founders will be able to cure Odo. It is revealed that the Founders had Weyoun infect Odo with the disease, necessitating his return. As punishment for killing a Changeling one year earlier, he is turned into a solid. (DS9: "Broken Link")
- Voyager is hijacked by the Kazon-Nistrim, assisted by Seska, and the crew is marooned on Hanon IV. (VOY: "Basics, Part I")
- The Terran Rebellion captures Terok Nor and begins constructing the ISS Defiant with the plans stolen from Deep Space 9 the previous year. (DS9: "Shattered Mirror")
- Regent Worf attempts to retake Terok Nor from the rebels, but is defeated in battle by the newly completed Defiant, commanded by Captain Benjamin Sisko of the prime reality. (DS9: "Shattered Mirror")
- VOY: "Parturition"
- VOY: "Relativity" (in part)
- DS9: "Rejoined"
- VOY: "Persistence of Vision"
- DS9: "Little Green Men" (in part)
- VOY: "Tattoo"
- DS9: "Starship Down"
- VOY: "Cold Fire"
- DS9: "The Sword of Kahless"
- DS9: "Crossfire"
- VOY: "Alliances"
- DS9: "Return to Grace"
- VOY: "Threshold"
- DS9: "Sons of Mogh"
- DS9: "Rules of Engagement"
- VOY: "Innocence"
- VOY: "The Thaw"
- DS9: "For the Cause"
- VOY: "Shattered" (in part)
- DS9: "The Visitor" (in part)
- VOY: "Basics, Part I"