In 2370, the station was the command post for Alliance authority throughout the Bajor sector, under the command of Intendant Kira Nerys. The station also served as a processing center for uridium ore mined from Bajor; the processing facilities were manned by Terran slaves.
In 2372, the Terran Rebellion wrestled control of the space station away from the Alliance. The Alliance, determined to recapture the station, sent a fleet of ships under Regent Worf's command to fight the rebels. When they arrived, the rebels had completed the ISS Defiant, which was based on schematics for the USS Defiant from the mirror universe. The Alliance fleet was defeated and Terok Nor remained a base of operations for the Terran Rebellion.