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The Provisional Government of Bajor invites Starfleet to help them rebuild after the Cardassian Occupation. Commander Benjamin Sisko is selected to take command of their space station, formerly known as Terok Nor that is then designated by Starfleet as Deep Space 9. As part of the agreement between the Federation and Bajor, Starfleet will help them to become a member of the Federation.

In their second year together, the crew of Deep Space 9 face problems that will affect the galaxy forever. A Bajoran extremist group attempts to force the Federation out of the Bajoran system. The Cardassians are secretly supplying them with weapons, hoping to return to reclaim the planet and hold the Bajoran wormhole for the Cardassian Union. However, the greatest enemy of all is lurking beyond it.

Season 3 of Deep Space Nine marks a turning point for the series, as it introduces the USS Defiant, a powerful starship that allows the crew to explore the Gamma Quadrant and face the threat of the Dominion, a vast and ruthless empire ruled by the shape-shifting Founders.

Season 4 of Deep Space Nine marks a major shift for the series, as it introduces a new conflict between the Federation and the Klingon Empire, sparked by the latter's distrust of the shape-shifting Founders. Worf, the former security chief of the USS Enterprise-D, joins the station's crew as Sisko's strategic operations officer, and faces challenges in his loyalty, honor, and family.

Season 5 of Deep Space Nine begins the Dominion War arc that will dominate the rest of the show. The Federation and its allies face a new enemy in the form of the Cardassian-Dominion alliance, which threatens to conquer the Alpha Quadrant.

Season 6 of Deep Space Nine marks the height of the Dominion War arc, as it depicts the Federation and its allies in a desperate struggle against the Cardassian-Dominion alliance, which has occupied Deep Space Nine and the Bajoran system.

Season 7 of Deep Space Nine marks the end of the series, as it concludes the Dominion War arc and the saga of the characters and their relationships. The Federation and its allies face the final showdown with the Cardassian-Dominion alliance, which is aided by the Breen. Sisko and his crew must also deal with the threat of the pah-wraiths, the evil counterparts of the Prophets, who are unleashed by Kai Winn and Dukat.