When the Cardassian Empire began the occupation of Bajor in the mid-24th century, they needed to set up military outposts throughout the region. One of the most central posts was built in orbit of Bajor and was named "Terok Nor." Gul Dukat and many other Cardassians stayed on "Terok Nor" to oversee ore production and other things while they forced the Bajorans to do the labor.

When Starfleet intervened and the Cardassians fell back from the Bajoran system, they raided Terok Nor and took everything of value and destroyed many key systems before evacuating the station. Starfleet was then invited to take over the station and help the Bajorans rebuild. Since the station was now under federation control, it was re-designated as Deep Space 9. DS9 was filled with Starfleet officers and member of the Bajoran military who helped make repairs to the station and slowly integrate Starfleet hardware and devices to make the foreign space station more suitable for its new occupants. The station was re-located away from Bajor to the wormole so that it could monitor traffic coming in or out of it at all times and take guard over the wormhole before the Cardassians or any other species found it first.

Deep Space 9 is of Cardassian design and thus is unlike other space stations and starbases in the Federation. The station is composed of a central core surrounded by an inner and outer ring, which houses the large claw-like docking pylons and smaller docking ports. The central core houses the control center of the station called Operations or "OPS", the multi-level promenade, crew quarters, and the central power and computer cores. The inner ring consists of crew quarters, weapons towers, and 6 docking bays which store the starfleet runabout shuttles. The outer ring holds mainly cargo bays, docking pylons and ports, and thrusters.

The control center of the station, OPS, is of typical cardassian design, something that Starfleet officers are not used to. The consoles are laid out in cardassian and are not easy to understand or operate. OPS is a multi-level structure that features stations for science, engineering, tactical, communications, and other important areas. It is also equipped with two open, large turbolifts and its own transporter pad. The front of OPS has a large cardassian viewscreen which is translucent. An office is located on the aft of the compartment, where the Cardassian Commander would normally reside. However, is has been designated as a ready room for the station commander.

Other important areas on the ship include the wardroom, a large place for meetings and conferences between the senior officers that features a long conference table and many computer displays for animating tactical strategies and other information; and the promenade, a multi-level space in the central core that could be described as a sort of "intergalactic shopping mall." The large promenade features many walkways and staircases to access the different areas located here, and there are also large viewports that allow pedestrians to view ships and the wormhole. Among places on the promenade are the security office, the infirmary, Quark's bar and holosuites, a tailor shop, and various alien restraunts and vendors.