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(covers information from Twilight universe)
The Starfleet Operating Forces are the collective Starfleet services under the command of the Commander-in-Chief and the Joint Chiefs of Staff, commanded from Starfleet Headquarters. It consists of the autonomous branches of Starfleet, the Starfleet Marine Corps, the Starfleet Starfighter Corps, and the Starfleet Intelligence Directorate, as well as the Directorate of Education.
Several independent divisions within Starfleet also fall under the auspices of Starfleet Headquarters under certain circumstances. The Starfleet Corps of Engineers frequently reports directly to Starfleet Headquarters, as do Starfleet Research and Development and the Starfleet Criminal Investigative Service. In disaster situations, the Federation Emergency Management Agency, a division of Starfleet Medical, also reports directly to the Commander-in-Chief.