Starfleet Command Starfleet Command , or Spacefleet Command , was the operating authority of Starfleet , the exploratory , scientific , and military department of United Earth before being integrated into the United Federation of Planets in 2161 . The organization ' s primary management center was located at Starfleet Headquarters in San Francisco , Earth . ( ; ; ) History . During the 22nd century and through the 23rd century , Starfleet Command was under the jurisdiction of the UESPA , notably during Captain James T . Kirk ' s era . Pre - Federation . In 2151 , captain Jonathan Archer met with Admiral Maxwell Forrest , Admiral Daniel Leonard , Commander , and other Human and Vulcan officials at Starfleet Command to decide how to proceed with delivering the wounded Klingon Klaang back to Qo ' noS . ( ) In 2152 , Archer was forced to return to Starfleet Command in order to decide how to proceed after " Enterprise " apparently destroyed the Paraagan II mining colony . ( ) In of 2153 , Forrest and Williams used Starfleet Command to coordinate the response to the crisis caused by re - activated Borg drone s . ( ) Later that month , " Enterprise " was recalled after the Xindi attack on Earth , and Archer went to Starfleet Command to discuss the attack , plan a response , and gain clearance to search for the Xindi weapon . ( ) After destroying the Xindi weapon in February of 2154 , Archer was debriefed by Forrest , Soval , and Williams about his actions in the Delphic Expanse at Starfleet Command . ( ) During shore leave later that year , Archer visited Starfleet Command again . ( ) Starfleet Command also housed a prison facility in the 22nd century . Arik Soong was incarcerated here for stealing Augment embryo s from Cold Station 12 . ( ) Starfleet Command was also host to the conference Nathan Samuels conducted to form the Coalition of Planets . The xenophobic organization Terra Prime planned to destroy the complex with a blast from the hijacked verteron array on Mars . The leader of Terra Prime , John Frederick Paxton , managed to fire the array after Archer , Malcolm Reed , Travis Mayweather , and Phlox launched a raid . However , thanks to sabotage by " Enterprise " chief engineer Charles Tucker III , the blast was redirected into San Francisco Bay . After the crisis passed , the conference resumed . ( ) Federation . Starfleet Command was overseen by the Federation Council and run by a chief of staff , a position held by Admiral Jonathan Archer in the late - 22nd century . Besides the fleet , Starfleet Command also oversaw the various other branches of Starfleet . Because of the time delays involved in many subspace communication s , Starfleet Command also included a network of administrative and support outpost s known as starbase s throughout the Federation . Starfleet ' s starship s operated out of these starbases under the supervision of various admirals , the senior officer s of the fleet . In 2286 , Starfleet Command , along with the rest of Earth , was threatened by the Whale Probe until Admiral Kirk and the crew of the late starship stole a Klingon Bird - of - Prey , which was renamed by Doctor Leonard McCoy . Kirk and his crew brought aboard a pair of Humpback whale s called George and Gracie . These whales were the prized attraction of the Cetacean Institute in Sausalito , California . Also brought aboard was marine biologist Gillian Taylor , an employee of the institute in 1986 . Kirk brought his new passengers back to 2286 , at which point the whales communicated with the probe ; it presumably returned to its place of origin . By 2364 , Starfleet Command had been infiltrated by parasitic being alien s , who had physically taken control of the bodies of several high - ranking Starfleet officials , including Admirals Gregory Quinn , Aaron , and Savar . The parasitic mother creature resided in the body of Lieutenant Commander Dexter Remmick . The aliens were prevented from taking over Starfleet Command by Captain Jean - Luc Picard and Commander William T . Riker of the , who , by destroying the mother creature , killed all alien parasites on the planet . ( ) In late 2373 , Starfleet Command made a decision that would change the Federation forever . They agreed with Benjamin Sisko that no more Dominion ships could be allowed into the Alpha Quadrant . The mining of the Bajoran wormhole became the catalyst of the Dominion War . ( ) In 2374 , Starfleet Command approved of Sisko ' s radical plan to bring the Romulan Star Empire into the Dominion War . ( ) Later that year , Starfleet Command honored Captain Sisko with the Christopher Pike Medal of Valor for his planning and successful operation retaking Deep Space 9 . ( ) After Captain Sisko contacted Starfleet Command about Section 31 , Starfleet Command did not acknowledge its existence , but did not deny it , either . Sisko was informed by Starfleet Command that they would look into it . The Starfleet Command investigation into Section 31 was later shelved . ( ) The order to quarantine a ship or station came from Starfleet Command . ( ) " In the alternate reality , Starfleet Command included an Office of Special Plans . " ( ) Personnel . Facilities . The following personnel were listed as working in the Facilities group on a personnel roster . ( ) " Enterprise " ( NX - 01 ) . The following personnel were noted for their work with Starfleet Command on in 2151 . ( , dedication plaque ) " Columbia " ( NX - 02 ) . The following personnel were noted for their work with Starfleet Command on in 2154 . ( , dedication plaque ) USS " Enterprise " ( NCC - 1701 - B ) . The following personnel were noted for their work with Starfleet Command on the on stardate 9715 . 5 . ( , dedication plaque ) USS " Enterprise " ( NCC - 1701 - D ) . The following personnel were noted for their work with Starfleet Command on the on stardate 40759 . 5 . The individuals listed were admiral s . ( , dedication plaque ) USS " Defiant " ( NX - 74205 ) . The following personnel were noted for their work with Starfleet Command on the on stardate 47538 . 5 . ( , dedication plaque ) USS " Voyager " ( NCC - 74656 ) . The following personnel were noted for their work with Starfleet Command on the on stardate 48038 . 5 . ( , dedication plaque ) USS " Enterprise " ( NCC - 1701 - E ) . The following personnel were noted for their work with Starfleet Command on the on stardate 49027 . 5 . ( , dedication plaque ) USS " Valiant " ( NCC - 74210 ) . The following personnel were noted for their work with Starfleet Command on the on stardate 49456 . 5 . ( , dedication plaque ) USS " Prometheus " ( NX - 59650 | NX - 74913 ) . The following personnel were noted for their work with Starfleet Command on the on stardate 50749 . 5 . ( , dedication plaque ) USS " Defiant " ( 2375 ) . The following personnel were noted for their work with Starfleet Command on the on stardate 52889 . 3 . ( , dedication plaque ) USS " Pasteur " ( NCC - 58925 ) . The following personnel were noted for their work with Starfleet Command on the . The individuals listed were admirals . ( , dedication plaque )