Commander Benjamin Sisko is assigned by Starfleet as station commander of "Deep Space Nine" in orbit of Bajor, previously used by the Cardassian Union during its occupation of the planet, now repurposed to help Bajor to enter into the Federation. Sisko is resentful of the duty, having lost his wife Jennifer three years previously during the Borg attack at Wolf 359 and destruction of his former ship, the USS Saratoga, and worried about the well-being of his teenage son Jake while on the station. When he and Jake arrive, they find the station nearly stripped bare of non-essential systems by the Cardassians, and the Bajoran staff, led by Major Kira Nerys distrusting of Starfleet's presence. As the USS Enterprise delivers more Starfleet staff, including Chief Miles O'Brien and his family, Sisko becomes more despondent of the position as he gets his final orders from Captain Picard, the man Sisko holds responsible for Jennifer's death. Sisko informs Picard of his intent to drop out of Starfleet to seek a civilian position in a few years, but continues to perform his job as station commander.
With the help of Odo, the station's chief of security, Sisko manages to convince the Ferengi barkeeper, Quark, to remain aboard the station, helping to keep the station as an active waypoint for ships as well as providing Jake a friend in Quark's nephew, Nog. He later visits the spiritual leader Kai Opaka on Bajor, who shows him the Orb of Prophecy and Change, one of several similar orbs believed to be sent by the Bajoran Prophets. Sisko looks into the Orb and finds himself reliving the moments when he met Jennifer for the first time. After his vision, the Kai tells Sisko that she believes him to be the "Emissary", a messiah figure that will help Bajor, and gives him the Orb to study further. When Sisko returns to the station, he finds the rest of his staff has arrived, including Chief of Medicine Dr. Julian Bashir and Science Officer Lt. Jadzia Dax, whom Sisko happily recognizes as a Trill and the current host of his former friend Curzon Dax. Sisko gives Dax the Orb to study to see if there is any scientific basis for the Orbs.
The station is soon visited by its former commander, the Cardassian Gul Dukat, who insists that he is seeking a way to regain his position and office back on the station, and remains in his ship parked in orbit near the station. When Dax discovers that the Orb is related to several phenomena near Bajor, Sisko recognizes that any investigation will tip off the Cardassians, and arranges for Odo to use his shapeshifting abilities to disable the Cardassian sensors. With the Cardassians unable to detect them, Sisko and Dax take a runabout to the location of the phenomena and discover the entrance to a stable wormhole leading to the Gamma Quadrant. Thrilled at the discovery, the two attempt to return through the wormhole but become stuck by some force inside it. Sisko and Dax are exploring the strange environment created for them inside the wormhole when Dax is suddenly sent away, appearing moments later on the operations deck of Deep Space Nine, while Sisko remains in a white void.