When the Cardassians abandoned the planet of Bajor, the United Federation of Planets was reluctantly called in by the new Bajoran provisional government to aid in the protection of their world from possible Cardassian reprisals. The Federation took control of the abandoned Cardassian ore refining station of Terok Nor and operations of the station was transferred to the Federation, under the supervision of Bajoran military liasons.

When the Bajoran wormhole was discovered, this new Federation outpost -- Deep Space 9 -- became a nexus of activity as scientists, colonists, and explorers from the Alpha and Beta Quadrants began probing the far reaches the distant Gamma Quadrant.

The importance of the base was again realized when the Dominion and their leaders, the Founders, began their campaign to invade and dominate the races of the Alpha and Beta Quadrants. Deep Space 9 quickly became the focal point for the conflict and was upgraded to the best equipment possible. The upgrades came just in time, as the station was forced to weather attacks from any number of hostile foes, including a massive Klingon assault on the station.

Though the station changed hands several times during the course of that war, Deep Space 9 remained a place of strategic importance. The station was finally reclaimed by Allied forces near the end of the Dominion War.

Following that war, the station continued operations, though under larger Bajoran control.