Flagship A flagship is a term referring to the status conferred upon a starship . Typically , a flagship is a starship commanded by a flag officer ( an admiral or similar rank ) . The term also properly applies to the ship of whatever commanding officer is in charge of a grouping of ships . A third , more colloquial usage of the term can mean that the ship in question is considered an " exemplar " of the best capabilities and virtues of the force it represents . United Federation of Planets . 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 2370 , the served as Vice Admiral Alynna Nechayev ' s flagship . ( ) In 2373 , 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 Admiral William Ross , who led from flagship during the Battle of Cardassia . ( ) Alternate timelines . In an unknown , alternate future timeframe , 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 . " " ( ) First Federation . In 2266 , the encountered the First Federation flagship " Fesarius " , under the command of Commander Balok . ( ) Klingon Empire . 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 warship s , 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 later promoted to Supreme Commander of the Ninth Fleet , following the recapture of Deep Space 9 in 2374 , Captain Benjamin Sisko offered to arrange the General quarters for him onboard the station . Martok declined , stating that " " I ' ll keep my flag aboard the " Rotarran " . It ' s cramped but at least I ' ll feel like I ' m still at war . " " ( ) The following year , Romulan Senator Cretak complained the low priority given to repairing Romulan ships , and that " " the " Dividices " and the " Genorex " have waited three weeks while a dozen Klingon ships have been given priority . " " Miles O ' Brien explained to the Senator that he planned the repair based on which ships had " " the greatest need " " , which so - happened to be the Klingon ships . Major Kira Nerys interrupted , and in the interest of diplomacy , agreed to allow the two ships in for repair , but to do so was required to delay repairs to the and the " Rotarran " , adding " " someone will have to tell General Martok why his flagship was bumped . " " ( ) Romulan Star Empire . In 2266 , the Praetor ' s flagship , " " the finest and proudest , " " in the Romulan Empire attacked several Earth Outpost Station s . 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 D7 class battle cruiser s 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 Warbird s 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 . " " ( ) 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 and worked to quell the alien rebellion . ( ) An was also in use during the 2250s . ( ) Klingon - Cardassian Alliance . Regent Worf commanded the Klingon flagship responsible for leading the assault , on several occasions , against and the Terran Rebellion . ( ) Alternate reality . In the alternate reality , the served as the flagship of Starfleet . ( ) Appendices . Apocrypha . According to the McDonald ' s comic " Star Trek Stars " , the was considered " command ship of the Federation " after the " V ' ger " incident .