(Note: stardates sometimes seem to be messed up somewhat, but i'm mentioning events in the order they're mentioned in Chronology. Where stardates are not given, none were mentioned in the episode.)

2372 2nd season Voyager, 4th season DS9 begin.
In "Non Sequitur" (sd. 49011), Harry Kim travels to an alternate universe in which he and Tom hadn't been on Voyager when it disappeared. He eventually returns to his own universe with the help of an extradimensional being.
Cardassian Central Command overthrown by civilians in the Detapa Council. Cardassian borders are closed; some outsiders believe the incident has been engineered by the Dominion.
Klingons declare war on Cardassia, and soon, the Federation, in "Way of the Warrior." The Defiant rescues members of the Detapa Council. Worf is assigned to Deep Space Nine as a consultant in dealing with the Klingons, and soon accepts a position as the station's strategic operations officer. Gowron strips Worf's family of all lands and titles, and has Kurn expelled from the High Council.
With the Cardassians weakened, the Maquis step up activity in the Demilitarized Zone.
In "The Visitor," Captain Sisko dies but is later prevented from having died by a much older Jake. In "Hippocratic Oath" (sd. 49066), Bashir tries to free renegade Jem'Hadar from their ketracel-white addiction. In "Indiscretion," Dukat finds his illegitimate half-Bajoran daughter, Tora Ziyal, and brings her to Cardassia. Kasidy Yates accepts a job as captain of a Bajoran Ministry of Commerce freighter.
Dukat is disowned by his mother, left by his wife, stripped of his rank, and reduced to piloting a small freighter, the Groumall, on which Ziyal lives with him.
In "Rejoined" (sd. 49195), Defiant personnel assist Trill scientists led by Lenara Kahn, in an attempt to generate an artificial wormhole. Much more work will be required. In "Little Green Men," Nog, who has recently been accepted to Starfleet Academy, sells his childhood possessions. Sam & Jax secretly buy some clandestine items which Nog feels it would not be appropriate for a Starfleet cadet to own. Gaila gives Quark a shuttle, which Quark names Quark's Treasure and uses it to transport Rom and Nog to Earth; however they accidentally end up in 1947, crashing in Roswell, NM. They later return to their own time, but Quark has to sell his shuttle as salvage. Rom and Quark return to DS9; Nog remains on Earth and enrolls at the Academy. In "Starship Down" (sd. 49263), the Defiant destroys two Jem'Hadar ships and rescues the crew of a Karemma vessel. In "Cold Fire," Suspiria wants Kes to join her and her Ocampa friends, who will help her develop her psychokinetic abilities. Kes declines, and Suspiria and the Ocampa are forced into a subspace domain they call Exosia. In "The Sword of Kahless," Worf, Dax, and Kor find the Sword of Kahless, which had been stolen by the Hur'q a millennium ago. But ultimately they release it into deep space in the Gamma Quadrant, believing the Klingon people are not ready for its return. In "Maneuvers," Seska helps Culluh steal a transporter control module from Voyager. Culluh attemps to unite several Kazon sects to attack and capture Voyager, but he is unsuccessful. Chakotay is temporarily captured by Culluh.
The Sovereign-class Enterprise-E is launched under the command of Captain Jean-Luc Picard.
In "Our Man Bashir," we first see a holoprogram wherein Dr. Bashir portrays a 20th century spy à la James Bond. Transporter patterns of various crew members accidentally get integrated as characters in the program.
A bomb disrupts a conference on Earth between the Romulan and Federation governments, killing 27 people including a Tholian observer. It is feared this is the start of a Dominion invasion. Starfleet begins taking drastic security measures. The Bajoran wormhole beings to act strangely, as if cloaked Dominion ships were coming through.
In "Homefront," Sisko, Dax, and Odo go to Earth to help deal with the Dominion threat. Sisko is made head of Starfleet security on Earth and works closely with Admiral Leyton. After a planetwide power failure, President Jaresh-Inyo declares a state of emergency and authorizes martial law under the command of Leyton. In "Paradise Lost," Sisko discovers that the power failure and the odd wormhole activity had been engineered by Admiral Leyton (utilizing the naive Red Squad cadets), who feared Jaresh-Inyo's leadership would be inadequate to face a Dominion threat, and attempted to initiate a coup d'etat. Once exposed, Leyton resigned from Starfleet. Jaresh-Inyo cancelled martial law.
In "Alliances" (sd. 49337), various Kazon sects attack Voyager. Janeway attempts to form a truce with them, but fails. Then she tries to form an alliance with the Trabe, who had formerly enslaved the Kazon. But they were a bunch of jerks, too, and Voyager remained all alone. in "Crossfire," Bajoran first minister Shakaar visits DS9 for talks about the timetable for Bajor's admission to the Federation, which are disrupted by Cardassian terrorist group the True Way. Meanwhile, Shakaar and Kira become romantically involved.
"Threshold" (sd. 49373). Apocryphal.
Tuvok discovers evidence that someone is covertly sending information to the Kazon-Nistrim. He devises and begins a ruse to uncover the spy.
In "Return to Grace," Klingons destroy an outpost on planet Korma where talks between Bajorans and Cardassians are being held. Dukat's freighter, the Groumall, is also destroyed, but Dukat captures the bird-of-prey which destroyed it and claims it for his own. He embarks on a campaign against the Klingons, against orders from the Detapa Council. Ziyal goes to stay with Kira on Deep Space Nine. In "Meld," it is discovered that Voyager crewman and former Maquis Lon Suder (a Betazoid) murdered crewman Frank Darwin. Tuvok mind-melds with him. Suder gains a measure of Vulcan discipline, but Tuvok is overcome by Suder's violent tendencies. Janeway orders Suder incarcerated for the remained of Voyager's return home. Tuvok continues tutoring Suder in Vulcan meditation techniques. In "The Sons of Mogh" (sd. 49556), it is discovered that the Klingons have placed cloaked subspace mines around the Bajoran system. Sisko orders them detonated to avoid their use against Bajoran traffic. Kurn asks Worf to perform the Mauk-to'Vor rite of death, but Worf is prevented from doing so by DS9 medical personnel. Instead, Bashir erases Kurn's memory and with the help of an old friend of Mogh's family, Noggra, a new identity is provided for Kurn, now called Rodek. 'Rodek' is told he suffered amnesia. In "Death Wish" (sd. 49301), Voyager personnel release a Q who will come to be called Quinn, from a cometary prison. Quinn is granted asylum on Voyager, but later ends his own life. In "Bar Association," Rom and Quark's other employees form a labor union, which the Ferengi Commerce Authority considers intolerable. The FCA sends Liquidator Brunt to deal with the situation. Quark takes care of it, no thanks to Brunt. Rom resigns his job at Quark's and takes a position as a diagnostic and repair technician on DS9's night shift. Worf moves his quarters from DS9 to the Defiant. In "Accession," Bajoran poet Akorem Laan, lost two centuries ago, emerges from the wormhole to claim the title of Emissary. He reinstitutes some sucky old caste system and stuff, and ultimately Sisko reclaims the title of Emissary and has the Prophets send Akorem back to his own time. In "Investigations" (sd. 49485), Tom Paris resigns his Starfleet commission and accepts a job as a pilot with a Talaxian convoy. Paris is then captured by the Kazon-Nistrim. It is discovered that Michael Jonas was the spy, who is killed in a Kazon attack on Voyager. Tom Paris returns to Voyager. In "Deadlock" (sd. 49548), a spatial rift creates a duplicate Voyager and crew. One ship is destroyed, though its Harry Kim as well as Samantha Wildman's newborn baby girl cross over to the surviving Voyager, to replace their counterparts, who had died on that ship. In "Rules of Engagement" (sd. 49665), Worf is put on trial for destroying a shipful of Klingon civilians while defending a Cardassian convoy. It is later discovered there were no people on the ship and that the incident had been engineered by the Klingon government in hopes of ending Federation protection of Cardassian convoys.
Miles O'Brien is convicted by the Argrathi of espionage and implanted with memories of 20 years of imprisonment. In "Hard Time," the psychological after-effects of these memories nearly drive O'Brien to suicide. However, he ultimately agrees to counseling and medication.
In the mirror universe, Terran rebels capture Terok Nor and imprison Intendant Kira. Garak flees the station and boards a Klingon warship commanded by Regent Worf. The rebels use stolen files from our universe to build their own Defiant.
In "Shattered Mirror," mirror-Jennifer Sisko takes Jake to her universe in order to get Sisko to follow and help get their Defiant operational. Worf's fleet is defeated by the rebels. Intendant Kira escapes and kills mirror Jennifer and mirror Nog. She spare's Jake's life so that she may collect the debt later from his father.
In "For the Cause," Kasidy Yates is arrested for smuggling supplies to the Maquis. Starfleet security officer Michael Eddington is found to be a member of the Maquis. He steals 12 industrial replicators the Federation was to donate to the Cardassians, and escapes capture. In "Tuvix" (sd. 49655), Tuvok and Neelix are combined into one person but later turned into their individual selves again. In "The Quickening," Bashir attempts to find a cure for a blight rendered on the population of a planet in the Teplan system, in the Gamma Quadrant, 2 centuries ago by the Jem'Hadar. He is unsuccessful, but develops a vaccine which may be used to innoculate unborn children.
Dominion scientists discover remains of an ancient Iconian gateway on Vandros IV, in the Gamma Quadrant. Renegade Jem'Hadar seize control of the site, and in "To the Death" (sd. 49904), Vorta agents enlist the aid of the Defiant to destroy the gateway, to protect both Federation and Dominion interests.
Quark goes to Ferenginar on a business trip. While there he is diagnosed with Dorek Syndrome and expected to live 6 or 7 days. Meanwhile, Kira, Bashir, and Keiko O'Brien go on a botanical survey mission to Tord V in the Gamma Quadrant. During the return flight, Keiko is severely injured. Bashir saves her life, but her unborn baby must be transplanted into Kira.
In "Body Parts," Quark returns to DS9 and sells his vacuum-desiccated remains in advance on the Futures Exchange, for 500 bars of latinum, to an unknown bidder who turns out to be Brunt. Quark then learns that he is not terminally ill, but Brunt still wants his remains. When Quark breaks his contract, Brunt revokes Quark's business license, seizes his family assets, and orders that Ferengi citizens may neither work at nor patronize Quark's bar. Quark's friends on DS9 help keep the bar in business. Kira moves in with the O'Briens for the term of her pregnancy.
The Federation asks the Klingons to give up Cardassian territory they had seized. The Klingons refuse, and demand that the Federation abandon all starbases in the Archanis sector.
In "Broken Link" (sd. 49962), Odo becomes ill and is forced to seek help from the Founders, who have caused his illness in order to get him home to face judgement for killing another Changeling. His punishment is to become a solid. Garak is sentenced to 6 months imprisonment for attempting to commandeer the Defiant's weapons to destroy the Great Link. Gowron suspends talks with the Federation and dispatches a task force to the Archanis sector. Odo tells Sisko he retains a memory from the Great Link that Gowron has been replaced by a changeling. In "Basics, Part I," Seska has recently given birth to a child she claims is Chakotay's, having stolen his DNA during "Maneuvers." Using the child as bait, she and Maje Culluh lure Voyager into a trap, strand the crew on a planet, and claim the ship for themselves. The only crewman left on board, unknown to the Kazon, is Lon Suder.

2nd season Voy, 4th season DS9 end, around sd.49999.
2373, 3rd season Voy, 5th season DS9 begin, around sd.50000.
2375, Mirror Gamma begins, sd.52359.
Mirror Gamma ends, around sd.52562.

26th century A researcher from this century travels to 22nd century Earth, where his time pod is stolen by Berlinghoff Rasmussen, an unsuccessful inventor who uses the pod to go to the 24th century, where he tries to steal technology to patent in his own time.

27th century Scientist Kal Dano invents the Tox Uthat, a quantum phase inhibitor which can halt all nuclear reactions within a star. Vorgon criminals attempt to steal it, so Dano travels to the 22nd century and hides the device on Risa, where it is unearthed by Picard and Vash in 2366.

29th century A temporal explosion is triggered by Voyager in the 20th century and destroys a bunch of stuff 900 years later, although all this is averted by Captain Braxton of the Federation timeship Aeon.

123rd century Radiation levels in the Andromeda galaxy are expected to reach intolerably high levels, according to scientists of the Kelvan Empire.

Stuff in darkred text has to do with the series "Enterprise," which may or may not be accepted as officially part of the Star Trek universe.

Stuff in black text can generally be assumed to be part of official Star Trek, usually if not always taken from the Chronology (Michael and Denise Okuda), or the various shows and movies.

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