In the mirror universe, Starfleet Command was the primary command post of Starfleet on Earth. It served the Terran Empire. It ran daily communiqués to Starfleet starships. (TOS: "Mirror, Mirror")

In 2155, Commander Jonathan Archer claimed to have received a private communiqué from Starfleet Command when he took over the command of the ISS Enterprise NX-01. (ENT: "In a Mirror, Darkly")

Archer blamed the rebellion on "criminals... sitting in their comfortable offices back at Starfleet Command." (ENT: "In a Mirror, Darkly, Part II")

In 2267, James T. Kirk (impersonating his mirror version) defied orders from Starfleet Command by delaying to destroy the Halkans. Starfleet Command then ordered Spock to wait one day to see if Kirk would follow his orders, and then kill him if he didn't, becoming the new captain of the ISS Enterprise NCC-1701. (TOS: "Mirror, Mirror")