Space Command is a large-scale space station that functions as the military headquarters of the Federation. It was run by Supreme Commander Servalan, and according to Par, is where the Federation is truly controlled from. (B: Trial).
The station recurs throughout the first two series as the primary location from which Servalan dispenses her orders, confers with Travis and her other lackeys and deals with the President's politicians trying to curb her power.
In the episode "Trial", the station is attacked by the Liberator and left in a damaged state. In "Star One", Servalan runs her coup from Space Command and assumes the presidency shortly before the Intergalactic War from Andromeda breaks off.
Due to Servalan's more active role in the field (and the dismanting of her office set), Space Command only makes one brief appearance in series 3, in the episode "Harvest of Kairos" and is not shown again thereafter.
In the Big Finish audio dramas, it is revealed that the Liberator destroyed Space Command on the orders of the rebel Avalon.