The Command Capsule was a craft used by the Marshal of Atrios in his attack on Zeos. It was the last surviving Atrion craft out of a fleet of hundreds.
The attack was prevented by the Fourth Doctor creating a time loop in which the marshal's order to fire was constantly repeated. The Doctor shrank the time loop to the area aroud the capsule and the Zeon control room.
The capsule was eventually released from the loop and fired a missile. The Doctor diverted it into the Third planet. (DW: The Armageddon Factor)