- Shadow Fleet formed, with its base of operations at Deep Space Station Discovery
- USS Discovery commisioned into Shadow Fleet, under Captain Kayla Harper
- USS Monitor attached to Shadow Fleet center of operations, DS Discovery
- Captain John Kawolsky takes command of the USS Discovery
- USS Discovery discovers Shadowous Station
- USS Discovery first learns of civil unrest in Cardassian territory
- Orion crisis begins
- USS Discovery becomes the second Federation starship to witness the collapse and expansion of two binary stars in the Omega IV system.
- Commander Scott Bradley seemingly killed in action against Romulans.
- Peace talks begin with the Orion Syndicate.
- USS Discovery is destroyed by the Orion Syndicate in a final stand.
- Orion Crisis ends
- The Akira-class USS Blackpool is commisioned into Shadow Fleet
- Admiral Chris O'Neill kidnapped from the DS Discovery, but shortly thereafter rescued by Captain Kawolsky on the USS Blackpool
- USS Blackpool renamed USS Discovery-A in honor of the first Starfleet vessel to bear the name.
- Commander Bradley discovered to have been kidnapped by Romulans, but rescued by the crew of the USS Discovery
- USS Discovery comes across large Sal'Tek fleet and is almost destroyed in the fighting, however it is rescued by the USS Monitor, under Admiral O'Neill
- Cardassian Civil War begins
- Scott Bradley takes command of the USS Atlantis
- Planet codenamed "Safehaven" discovered for Cardassian settlers and government.
- USS Discovery and USS Atlantis forced from SafeHaven leaving many crewmembers behind.
- USS Discovery and USS Atlantis return and rescue the stranded crewmembers.
- Cardassian Civil war ends, and Scott Bradley returns to the USS Discovery
- USS Discovery makes first contact with the warlike Telonians, and several crewmen are kidnapped
- USS Discovery transported to the far reaches of the Beta Quadrant.
- USS Discovery rediscovers the extinct Iconian species, and the sleeper agents appear for the first time.
- USS Discovery returns home to the Alpha Quadrant
- Iconian War commences
- A large Federation fleet, accompanied by the USS Discovery, destroys a major Iconian staging vessel, setting back their war effort
- DS Discovery renamed Blaisdell Station and Commander Riley T. Munro appointed Commanding Officer.
- Blaisdell Station attacked by a large Iconian fleet. The USS Discovery is mobilised to defend it. Several sleeper agents activated onboard the Discovery
- USS Repulse commisioned, under command of Commander Richard Ransom
- USS Repulse encounters the rogue Vulcan T'vek
- USS Intrepid commissioned, under command of Captain Jacob Hannagan
- USS Discovery finds a damaged Iconian ship, and it is discovered that the sleeper agents onboard the Discovery are the historical leaders of the Iconian people, the Draynar
- Blaisdell Station destroyed by an imposter posing as Starfleet Admiral Hansen, killing several crewmen
- Starbase 83 becomes Task Group Alpha Headquarters
- USS Repulse transported to alternate timeline, in which Starfleet has lost the Iconian War
- Romulus destroyed by a supernova
- USS Intrepid transfered out of Shadow Fleet
- USS Repulse defeats T'veks plans to ignite a civil war in the Federation
- USS Repulse destroyed, with T'vek on board
- USS Port Royal commissioned under command of Captain Riley T. Munro
- USS Discovery encounters a rogue Iconian faction, and begins negotiations
- USS Port Royal finds and kills the imposter who destroyed Blaisdell Station
- Iconian war ends after approximately 500 days of fighting, with millions of casualties on both sides
- USS Port Royal destroyed in combat after an imposter beams aboard and discharges a phaser in engineering
- Commander Scott Bradley takes command of the USS Discovery after John Kawolsky is promoted to Rear Admiral (Lower Half)
- USS Discovery transported to an alternate timeline, where it encounters and fights the Borg
- USS Churchill commisioned, under command of Commander Alexander Clarke
- Commander Clarke is kidnapped by pirates. Mike Cortez takes command of the Churchill
- Pirate crisis begins
- The crew of the USS Discovery arrested by Starfleet and held for questioning.
- Commander Clarke rescued and resumes command
- USS Discovery returns to earth and encounters strange phantoms.