(covers information from several alternate timelines)
This page contains information regarding Star Trek: Discovery, and thus may contain spoilers.
A flagship was a term referring to the status conferred upon a starship. Typically, a flagship was a vessel commanded by a flag officer (an admiral or similar rank). The term was also properly applied to the ship of whichever commanding officer was in charge of a grouping of ships. A third, more colloquial usage of the term could mean that the ship in question was considered an "exemplar" of the best capabilities and virtues of the force it represented.
United Federation of Planets
The USS Enterprise-D served as the "flagship of the Federation" and of Starfleet, from 2364 to 2371. (TNG: "The Icarus Factor", "Sarek", "The High Ground", "Remember Me", "Ensign Ro", "Man of the People", "Chain of Command, Part I", "Starship Mine", "Force of Nature", "Parallels"; Star Trek Generations; DS9: "Bar Association")
While commanding the USS Sutherland, Data made continuous reports to the Enterprise-D, the flagship of the armada that employed the tachyon detection grid along the Klingon-Romulan border in 2368. (TNG: "Redemption II")
In 2373, Vice Admiral Hayes led the Federation fleet against a Borg cube at the Battle of Sector 001 aboard his flagship. Following its destruction, Jean-Luc Picard, captain of the USS Enterprise-E, took command of the fleet in order to coordinate the destruction of the cube. (Star Trek: First Contact)
The USS Defiant frequently served as a flagship during the Dominion War with Captain Benjamin Sisko leading attack fleets into Dominion-held space, although overall theater command was under Vice Admiral William Ross, who led from his own flagship during the Battle of Cardassia. (DS9: "Favor the Bold", "Sacrifice of Angels", "Tears of the Prophets", "The Changing Face of Evil", "What You Leave Behind")
In the anti-time future, Admiral William T. Riker commanded the Enterprise-D as his flagship explaining that "they tried to decommission her about five years ago. One of the advantages of being an admiral is you choose your own ship." (TNG: "All Good Things...")
In the late 23rd century the K't'inga-class battle cruiser Kronos One served as the flagship of Chancellor Gorkon. In 2293 it was carrying Gorkon for a rendezvous with the Federation starship USS Enterprise-A where it would be escorted to Earth for a peace conference. It was fired upon by an experimental Bird-of-Prey leading to a rescheduling of the conference. (Star Trek VI: The Undiscovered Country)
At one time during Romulan Commander Toreth's illustrious career, she commanded a ship that attacked a Klingon outpost which was supposedly undefended, but was discovered to in fact be defended by an attack force of cloaked warships, that took her squadron completely by surprise. Half of her ships were destroyed before the Romulans even opened fire, but when they did, the Klingon ships were no match for the Romulans. In fact, Toreth even destroyed the Klingon flagship herself, following the assault, she received the Sotarek Citation for her actions that day. (TNG: "Face of the Enemy")
For five years of Martok's civilian career, he served as a laborer aboard ShiVang's flagship. As he explained it, "then, as fortune would have it, the Romulans made a foolhardy attempt to board our ship. I earned a battlefield commission." (DS9: "Once More Unto the Breach")
When General Martok was promoted to Supreme Commander of the Ninth Fleet following the recapture of Deep Space 9 in 2374, Captain Benjamin Sisko offered to arrange quarters for him on the station. Martok declined, stating "I'll keep my flag aboard the Rotarran. It's cramped but at least I'll feel like I'm still at war." The Rotarran was still Martok's flagship as of late 2375. (DS9: "You Are Cordially Invited", "Inter Arma Enim Silent Leges")
Romulan Star Empire
In 2266, the Praetor's flagship, "the finest and proudest" in the Romulan Empire, attacked several Earth Outpost Stations. It was successfully beaten by the USS Enterprise under the command of Captain James T. Kirk, and eventually destroyed by the ship's own commander in defeat. (TOS: "Balance of Terror")
The USS Enterprise encountered and was initially captured by a group of ships including two Romulan D7-class battle cruisers and a Bird-of-Prey after illegally crossing the Romulan Neutral Zone in 2268.
In 2370, Romulan and Federation task forces built up along the Romulan Neutral Zone in response to anomalous readings in the Devron system, located within the Zone. Four Warbirds held position along the Romulan side of the Neutral Zone, led by the flagship Terix commanded by Tomalak. (TNG: "All Good Things...")
The ISS Charon, launched in 2255, was the Imperial flagship and also housed Emperor Philippa Georgiou's Imperial palace. (DIS: "The Wolf Inside", "Vaulting Ambition", "What's Past Is Prologue", "Terra Firma, Part 1")
In the mid-2370s, Regent Worf commanded the Klingon-Cardassian flagship responsible for leading the assault, on several occasions, against Terok Nor and the Terran Resistance Forces. This flagship resembled a Negh'Var warship, but was built on a much larger scale. (DS9: "Shattered Mirror", "The Emperor's New Cloak")
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