Flagship
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  served as the "flagship of the Federation" and of Starfleet around 2259. ()

The  served as the "flagship of the Federation" and of Starfleet, from 2364 to 2371. (, , , , , ; ; )

While commanding the , 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. ()

During the Borg threat of 2369, the  served as Vice Admiral Alynna Nechayev's flagship. () 

In 2373, Vice Admiral  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 , took command of the fleet in order to coordinate the destruction of the cube. () 

The  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. ()

Alternate timelines 
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." ()

Alternate reality
In the alternate reality, the , launched in 2258, served as the flagship of Starfleet. ()

First Federation
In 2266, the  encountered the First Federation flagship Fesarius, under the command of Commander Balok. ()

Klingon Empire
In the late 23rd century the  battle cruiser Kronos One served as the flagship of Chancellor Gorkon.  In 2293 it was carrying Gorkon for a rendezvous with the Federation starship  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. ()

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. ()

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." ()

In 2372, the Klingon Empire introduced the  as its new flagship. ()

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. ()

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. ()

The USS Enterprise encountered and was initially captured by a group of ships including two Romulan  battle cruisers and a Bird-of-Prey after illegally crossing the Romulan Neutral Zone in 2268. 

After a series of deceptions on the part of Kirk and Spock aboard the Romulan flagship, they were successful in stealing its cloaking device. ()

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. ()

In 2375, during the Battle of Cardassia, Admiral William Ross reported to Captain Sisko that "the Romulan flagship's been destroyed. Their entire line is collapsing." ()

R'ongovian Protectorate

In 2259, the flagship of the R'ongovian Protectorate was an antiquated solar sailship only used for ceremonial occasions. Per R'ongovian custom, after a treaty was signed, the ship would fly the flag of their new allies as a tribute. ()

Emerald Chain

In 3189, the heavy cruiser Viridian served as the flagship of Osyraa, leader of the Emerald Chain. ()

Mirror universe

Terran Empire

In the mirror universe, in 2155, the  served as the flagship of the Terran Empire. () 

Later,  declared the  his flagship after he captured it from the Tholians and planned to take over the Empire. ()

The , launched in 2255, was the Imperial flagship and also housed Emperor 's Imperial palace. ()

Klingon-Cardassian Alliance

In the mid-2370s, Regent  commanded the Klingon-Cardassian flagship responsible for leading the assault, on several occasions, against  and the Terran Resistance Forces. This flagship resembled a Negh'Var warship, but was built on a much larger scale. ()

Appendices

See also 
Lead ship

Apocrypha
According to the McDonald's comic "Star Trek Stars", the  was considered "command ship of the Federation" after the V'ger incident.

External links

de:Flaggschiff
ja:旗艦
nl:Vlaggenschip
sv:Flaggskepp
Spacecraft classifications