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. Source: Memory Alpha

In Star Trek: Theurgy, Starfleet Command has been compromised by an unknown enemy, replacing the people in the upper echelons of this institution. It is unknown what other bodies of power in the galaxy have been infested with the alien influence.