Three years later, a reluctant Sisko and his even more reluctant son are transferred to the space station Deep Space Nine in Bajoran territory. Now a Commander, Sisko has been ordered to oversee the repair of the giant space station, which was heavily damaged during a period of Cardassian military occupation.

After his arrival, Sisko begins to meet his crew. He first encounters Chief Operations Officer Miles O'Brien, who has been transferred from the Enterprise, and Kira Nerys, a Bajoran who helped lead her people's painful fight against the Cardassians. Kira agrees to act as Sisko's first officer, but has reservations about the Federation's presence on the Bajoran space station. Soon afterward, he meets Odo, a shape shifter and security officer who exhibits his chameleon-like talents while apprehending a Ferengi thief. Quark, the Ferengi owner of the local watering hole and gambling establishment, arrives to bail out the thief — his young nephew, Nog. Sisko agrees to free Nog only if Quark will remain aboard and continue to operate his recreation center for the station's residents and visitors.

The Enterprise docks at Deep Space Nine, and Sisko has a tense meeting with Picard, whom he blames for the death of his wife. Picard tersely informs Sisko that his mission aboard the space station is to assure the Bajora enter the Federation. Sisko indicates that while he will do his job as long as he is there, he may resign his post. The two part on less-than-friendly terms. Sisko looks to Kira for insight into the Bajora, and she tells that his only chance for success is for the Bajora, a somewhat diverse group, to find reason to unite. She suggests that he seek out Kai Opaka, the Bajoran spiritual leader, and Sisko immediately sets out to find her. Kai Opaka reveals that Sisko's arrival has a deep spiritual purpose, but is unable to reveal exactly what it is. She entrusts Sisko with a powerful and mystical orb, telling him his destiny is to reclaim eight other orbs stolen by the Cardassians. To demonstrate the orb's power, Kai Opaka uses it to transport Sisko to the beach where he first met his wife.

Back on Deep Space Nine, Sisko greets his new crew of medical and science officers, including Dr. Julian Bashir, a cocky and ambitious young doctor, and Jadzia Dax, a beautiful Trill. Sisko's relationship with Dax is complicated by the fact that, as a Trill, she lives by inhabiting different host bodies. She and Sisko were close friends while she inhabited her previous body — that of an old man. In the laboratory, Sisko shows Dax the orb and explains they must find the eight others. When Sisko leaves, Dax experiences the orb's immense power when it takes her back to an earlier time, just as it did with Sisko.

Before long, the Enterprise disembarks and a Cardassian warship arrives at the station. The Cardassian leader, Gul Dukat, immediately tries to convince Sisko to relinquish the orb, but Sisko denies knowing anything about it or the other orbs. Later, Dax researches the orbs' history and informs Sisko that they may come from the nearby Denorios belt.

Dax and Sisko set out for the Denorios belt in a runabout. Without warning they are propelled through a giant tear in the fabric of space — a wormhole. After a spectacular light show, the pod slips out of the wormhole and into another corner of space — 70,000 light years from Bajor. Realizing this may be the venue the orbs entered their system, Sisko and Dax re-enter the wormhole to return home and study the implications. However, they land on a remote planet where an orb captures Dax and transports her back to Deep Space Nine. Dax immediately informs the others of her journey, exciting all of them with the possibilities the discovery presents. Kira demands that they transport Deep Space Nine to the mouth of the wormhole so the Bajorans may claim and operate the wormhole and gain power over the Cardassians. But Odo, who was discovered in the Denorios belt and does not know of his origins, has mixed feelings about the wormhole and the link it may provide to his past.

Left alone on the strange planet, Sisko communicates with the awesome force behind the orbs, who first perceive him as a threat. The force does not understand linear time, and presents Sisko with a barrage of images from his life, including the day he met his wife, Jennifer, and the battle where she was killed. Sisko is able to communicate with the alien images of Jake and his late wife. Soon after, Sisko and the force begin to understand each other.

O'Brien begins the task of maneuvering the space station to the mouth of the wormhole, but a Cardassian ship reaches it first. However, the mouth of the wormhole collapses around the alien ship, stranding it in a remote part of the galaxy. The alien force detects the Cardassian ship's presence and informs Sisko that they are no longer alone. However, the force continues to communicate with Sisko, indicating that he is trapped at the moment in time when his wife was killed aboard the Saratoga. Realizing his pain has been holding him back, Sisko allows the force to guide him through the circumstances leading up to his wife's death and helps him to finally grieve for his loss.

Aboard Deep Space Nine, Kira is contacted by Cardassian leader Gul Jasad, who accuses the station crew of destroying the lost Cardassian ship. The crew denies the accusation, but Jasad declares war, prompting Kira to launch an attack against the enemy. The battle escalates and the space station is damaged, but the wormhole suddenly reappears. Sisko's runabout is seen towing the Cardassian ship out of danger, and the fighting ceases.

Later, a changed Sisko speaks with Picard about the events of the past few days. He decides to keep his post on Deep Space Nine, and Picard agrees. Later, he speaks with Kai Opaka, who informs Sisko that this is not the last time he will work with the Bajoran prophets to secure the future of the space station inhabitants.