In the vicinity of the liberated planet of Bajor, the Federation space station Deep Space Nine guards the opening of a stable wormhole to the far side of the galaxy.

After a brutal decades-long occupation by Cardassians, the Bajorans requests Starfleet and the Federation come in to assist with rebuilding their world and society after the Cardassians' withdrawal from Bajoran space. Starfleet uses the old Cardassian space station orbiting Bajor, Terak Nor, now rechristened Deep Space Nine, as their new headquarters to oversee the recovery. The new commanding officer, Benjamin Sisko and Lieutenant Dax, discover the entrance to a stable wormhole leading to the galaxy's Gamma Quadrant, 60,000 light years away, that is anything but natural. In the wormhole reside beings existing outside of time the Bajorans have come to worship as the Prophets. As a result, the Bajoran people declare Sisko to be the Emissary of the Prophets. Sisko is largely uneasy about this, due in no small part to his Starfleet career, and being an outsider to the Bajorans. This also doesn't sit well both Starfleet, who view this as interference in their culture, and some Bajoran religious figures, who see an outsider as the Emissary as nigh sacrilegious. Sisko does his best to tread carefully between his roles as a Starfleet Officer following orders to help Bajor recover and with being the Emissary, all while trying to comply with Starfleet's Prime Directive of non-interference. The crew eventually discover that the Gamma Quadrant is controlled by The Dominion. The Founders, a race of shape-shifting aliens, created The Dominion to bring order to the galaxy, as well as creating the Jem'Hadar, genetically-engineered and ruthlessly efficient foot soldiers unconcerned with the conventions of war, as well as the genetically enhanced Vorta, who oversee The Dominion's day to day operations, and give orders to the Jem'Hadar. The Cardassians, who have been a thorn in the side of the Federation for decades, eventually ally themselves with The Dominion, declaring war on the Federation, the Klingons, and other races, to further bring The Dominion's form of order to the Alpha Quadrant, but they quickly realize this to not be the saving grace they had hoped for. The Federation-Klingon alliance must also resort to unconventional, and occasionally extreme, means to ensure the final victory, which comes at immense cost.

The stable wormhole discovered by the Deep Space Nine crew is known to the Bajoran people as the Celestial Temple of their Prophets. Sisko, as discoverer of the wormhole and its inhabitants, is therefore the Emissary of Bajoran prophesy. The wormhole's other end is in the Gamma Quadrant, halfway around the galaxy from Bajor. That section of space is dominated by the malevolent Dominion. The Dominion is led by the Changelings, the race of shapeshifters to which Odo belongs. As of the beginning of the sixth season, Cardassia has joined the Dominion, and together they are waging war on the Federation and their Klingon allies. The war is quickly becoming the most costly war ever for the Federation, and the Deep Space Nine crew must fight to protect their way of life.—Matthew D. Wilson <[email protected]>