- Starfleet introduces a new combadge with a gold rectangle with a cutout oval in the center replacing the gold oval. (DS9: "The Search, Part I", Star Trek Generations, VOY: "Caretaker")
- The Federation, as well as the other Alpha and Beta Quadrant powers, become aware of the Dominion threat after the USS Defiant returns from its mission to the Founders' homeworld in the Gamma Quadrant, the home of the designated leaders of the Dominion. (DS9: "The Search, Part II")
- The Obsidian Order exposes Legate Tekeny Ghemor's ties to the Cardassian dissident movement. (DS9: "Second Skin")
- The starship USS Equinox disappears, pulled into the Delta Quadrant by the Caretaker. The ship sets a return course to the Alpha Quadrant, but encounters the Krowtonan Guard, becoming severely damaged while losing half of its crew. (VOY: "Equinox")
- The starship USS Voyager departs Deep Space 9 on a mission to find the Maquis raider Val Jean. Both ships are thrown 75,000 light years into the Delta Quadrant by the Caretaker. The Caretaker's array, the only means home, is later destroyed by Captain Kathryn Janeway in order to protect the Ocampa and the two crews are forced to work together to find a route back to the Alpha Quadrant. (VOY: "Caretaker")
- Several crew members on Voyager, including first officer Cavit, flight controller Stadi, the chief medical officer, and the chief engineer, are killed during the transit to the Delta Quadrant. (VOY: "Caretaker")
- Deep Space 9 is spared destruction by mere seconds after a legacy counter-insurgency program installed by the station's original Cardassian commander is inadvertently initiated. (DS9: "Civil Defense")
- Captain Janeway grants field commissions to the Maquis crew. She assigns Commander Chakotay as her first officer and Lieutenant B'Elanna Torres as her chief engineer. Tom Paris is given the field commission of lieutenant and assigned to the conn. The ship's EMH, otherwise known as The Doctor, is assigned as chief medical officer. (VOY: "Parallax")
- The Maquis member Thomas Riker steals the USS Defiant and uses it to expose a Cardassian military buildup in the Orias system. (DS9: "Defiant")
- In an alternate timeline, Voyager discovers a Class M planet devastated by an explosion due to the detonation of polaric ion energy. Captain Janeway and Tom Paris are thrown back in time before the explosion by a subspace fracture. Janeway is able to revert the timeline so they return to Voyager and the civilization is spared. (VOY: "Time and Again")
- With help from Bareil Antos, Kai Winn and Legate Turrel sign the Bajoran-Cardassian Treaty. It sends political shock waves throughout the Alpha Quadrant. Bareil Antos dies soon after. (DS9: "Life Support")
- The Romulan Star Empire sends Ruwon and Karina to DS9 to take possession of Starfleet's data on the Dominion. This was agreed upon earlier in the year, in exchange for allowing the USS Defiant to operate a cloaking device. The Romulans also send a Warbird, intending to destroy the station and the wormhole. However, their plan is thwarted by Miles O'Brien, who had foreseen the future and warned Benjamin Sisko. (DS9: "Visionary")
- Voyager discovers a micro-wormhole. The crew sends in a microprobe, which reveals the wormhole leads to the Alpha Quadrant. Voyager, using the probe as a relay for a message, contacts a Romulan science vessel named Talvath, commanded by Telek R'Mor. However, it is later found out that the wormhole is a rift through time and that R'Mor is from the year 2351. After some consideration, R'Mor agrees to take the crew's personal messages with him and deliver them to Starfleet at the appropriate time. R'Mor is later discovered to have died in 2367 and the messages were apparently never delivered to Starfleet. (VOY: "Eye of the Needle", "Message in a Bottle")
- Voyager's Tom Paris is convicted of murdering the Banean Tolen Ren. After much evidence gathering, Tuvok is able to prove Paris' innocence and reveals a Numiri plot to steal Ren's technology. (VOY: "Ex Post Facto")
- The USS Enterprise-D is destroyed over Veridian III. Almost the entire crew survives in the ship's saucer section after the ship's separation, which crash lands on the planet after the ship's stardrive section exploded. (Star Trek Generations)
- Captain James T. Kirk emerges from the Nexus and is killed helping Jean-Luc Picard prevent Dr. Soran from destroying the Veridian system. (Star Trek Generations)
- Seska's true roots as a Cardassian spy are revealed. She betrays the Voyager crew and joins the Kazon. (VOY: "State of Flux")
- The Cardassian Obsidian Order together with the Romulan Tal Shiar are lured into a trap, when they attack the Founder's homeworld in the Gamma Quadrant. The following battle leads to the complete destruction of the combined Romulan-Cardassian fleet of twenty ships and severely cripples both organizations, which, in turn, reduces possible resistance against the Dominion by the Federation and the Klingon Empire. (DS9: "The Die is Cast")
- The Bajoran Shakaar Edon, a former cell leader in the Bajoran Resistance, becomes first minister of Bajor's provisional government. (DS9: "Shakaar")
- Reginald Barclay transfers to Jupiter Station and works at Dr. Lewis Zimmerman's holographic laboratory to test the Emergency Medical Hologram's interpersonal skills. (VOY: "Projections")
- Ensign Samantha Wildman discovers she is pregnant while stranded in the Delta Quadrant on Voyager. (VOY: "Elogium", "Fury")
- The USS Olympia crashes on a planet in Rutharian sector. Captain Lisa Cusak's distress call is sent three years into the future by the planet's energy barrier and is intercepted by the USS Defiant. Captain Cusak dies on the planet. (DS9: "The Sound of Her Voice")
- It is revealed that the Founders of the Dominion have infiltrated the Alpha Quadrant. (DS9: "The Adversary")
- Martok is captured by the Dominion on Kang's Summit and sent to Internment Camp 371. (DS9: "In Purgatory's Shadow")
- Voyager lands on a planet in the Delta Quadrant and discovers a colony of Humans, including Amelia Earhart, transported to the planet by the Briori centuries prior. (VOY: "The 37's")
- Benjamin Sisko is killed by the Klingon-Cardassian Alliance. Miles "Smiley" O'Brien recruits the prime universe Benjamin Sisko to take his counterparts place temporarily. (DS9: "Through the Looking Glass")
- Smiley steals the design schematics for the USS Defiant during his visit to Deep Space 9. (DS9: "Through the Looking Glass")
- Jennifer Sisko defects to the Terran Rebellion. (DS9: "Through the Looking Glass")
- VOY: "Parallax"
- VOY: "Time and Again"
- VOY: "Phage"
- DS9: "Destiny"
- VOY: "The Cloud"
- VOY: "Eye of the Needle"
- Star Trek Generations (in part)
- DS9: "Explorers"
- VOY: "Jetrel"
- DS9: "Family Business"
- VOY: "Learning Curve"
- DS9: "The Adversary"