The Battle of Chin'toka has decimated the Federation. Of all starships assigned to the campaign, only one survived the Breen onslaught. The Klingon Bird of Prey that did survive has allowed the Federation-Klingon-Romulan Alliance to come up with a partial way of defending themselves. Fortunately for them, the Cardassians have risen up against their former allies, buying Starfleet and the Romulans time to develop defenses agains the Breen's weapons. In an effort to help the Cardassians, Sisko sends his best officer to aid them in throwing off their Dominion oppressors: Colonel Kira Nerys.
When the Cardassian occupation of Bajor ended in 2369, the mining space station Terok Nor was left abandoned, its systems ripped out. By invitation of the Bajoran provisional government, Starfleet stepped in to oversee the rebuilding and day-to-day operations of the newly christened Deep Space Nine.
The years of Starfleet's nonintervention into Cardassian matters, however, had taken its toll on relations with the Bajorans. Consequently, Starfleet's position was a tenuous one; many Bajorans, suspicious and hostile as a result of decades of Cardassian oppression and brutality, did not greet the Federation's presence with open arms. The Federation's assistance is put to the test as DS9 becomes a center of travel and commerce that stretches into the Gamma Quadrant.