Command
From FreeSpace Wiki
Allied Command (most frequently referred to only as Command) oversees operations conducted by the Galactic Terran-Vasudan Alliance and gives orders to pilots and miscellaneous combat craft that participate in them.
The identity of Allied Command in neither FreeSpace is known. In Conflict: FreeSpace – The Great War, Allied Command is a human of Caucasian etnicity. Its head animation is Head CM-1, which is the only head animation used for larger ships in the first game. In FreeSpace 2, Command has head animation #2, who is a dark-skinned human.
Over the course of the two games, the player character gets reassigned to numerous new flagships, but these reassignments don't affect how Allied Command is portrayed.