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 two 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 unessential systems by the Cardassians, and the Bajoran staff, led by Major Kira Nerys, distrustful 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 that he is contemplating resigning from Starfleet to seek a civilian position, but continues as ordered to perform his job as station commander.
With the help of Odo, a shapeshifter who is 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 who 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 for a scientific explanation of the way it works.
The station is soon visited by its former commander, the Cardassian Gul Dukat, who was also the last Cardassian prefect of Bajor. Dukat informs Sisko that he has his ship parked in orbit near the station and asks permission for his crew to visit the station's promanade - Which Sisko grants. Later, 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 revealed 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.
Dax quickly relates their findings. Kira, recognizing the value of the stable wormhole to Bajor's future, orders the staff to move the station close to the wormhole's mouth. Gul Dukat, having repaired his sensors, follows the station and discovers the wormhole himself. Dukat enters the wormhole, but when the station's staff tries to follow, they find the wormhole entrance no longer open. Cardassian ships begin to arrive at the station, questioning the disappearance of Gul Dukat and dismissing the claims of a wormhole. After requesting help from Starfleet, Kira attempts to hold off the Cardassians' by altering their sensor reading to appear that the station is heavily armed. The Cardassians eventually see through the illusion, and prepare for an assault.
Sisko, in the meantime, finds that he has encountered entities in the wormhole who speak to him through images of his wife, friends, and crew members. The "wormhole aliens" question Sisko's corporeal and linear existence, and explain that they become disrupted when such beings pass through the wormhole. They become further enraged when Gul Dukat's ship attempts to pass through, and forcibly close the wormhole and disable the ship. Sisko attempts to explain how his kind thrive on their linear existence, but the entities point out that he continues to return to the moment of Jennifer's death. Sisko comes to the realization that he has been grieving over the loss of his wife and explains this to the aliens.
The Cardassians begin their attack on Deep Space Nine, but just as the shields fail and Kira prepares to surrender the station, the wormhole opens up again, with Sisko in the runabout towing Gul Dukat's ship out of it. On Gul Dukat's orders, the Cardassians stop their attack and depart from the sector. Sisko reveals that he was able to negotiate with the wormhole aliens to keep it open and allow ships to pass through. When the Enterprise arrives in response to Kira's earlier call for help, Sisko informs Picard that he plans to remain station commander indefinitely.