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(covers information from several alternate timelines)
Starfleet Command Headquarters and Starfleet Academy eventually occupied the Presidio, as well as grounds north of the Golden Gate Bridge in Marin County. Mindful of the site's history, Starfleet maintained the ancient coastal defense installation "Fort Point", as well as the iconic Golden Gate Bridge (completed in 1937) until its catastrophic damage in the Breen attack of 2375. (Star Trek: The Motion Picture; DS9: "The Changing Face of Evil"; VOY: "Endgame")
In the alternate reality, Starfleet Headquarters was not located at the Presidio; instead, it was located at Second Street. The Presidio was the home for Starfleet Academy and several shuttle hangars. In 2259, its location in San Francisco was seen on a map of the San Francisco Bay that was displayed on a powerwall in the office of Admiral Alexander Marcus. (Star Trek; Star Trek Into Darkness)