We meet Commander Benjamin Sisko, who is assigned to command DS9, but appears reluctant to do so. Sisko has a son, Jake, who also seems reluctant about living on the space station. Sisko's wife, Jennifer, was killed during the attack at Wolf 359, and we see that Sisko has not forgiven Captain Picard for his role in it, when Picard gives Sisko his orders: as commander of the station, Sisko is to work to prepare Bajor to join the Federation.

Upon arriving at DS9, Sisko meets Major Kira Nerys, a Bajoran woman who is to act as liaison between the Federation and Bajor, and Odo, the chief of security on DS9, who is a shape-shifter. We also learn that Miles O'Brien, previously a member of the crew of the Enterprise, will join DS9 as chief of operations. Quark, a Ferengi, runs a gambling establishment, and although he had intended to leave the station, Sisko convinces (or perhaps it would be more accurate to say 'coerces') him to stay. Later, Julian Bashir, the station's chief medical officer, and Jadzia Dax, a friend of Sisko, arrive, and the main cast is complete.

In order to fulfill his mission to prepare Bajor to join the Federation, Sisko must attempt to stabilize the government. Kira opines that the only way that will happen is if Kai Opaka, a spiritual leader on Bajor, were to assist. So, Sisko heads to Bajor to meet with her, and she tells him that he will be the Emissary of the Prophets, the Bajoran gods. She shows him a glowing object she calls a Tear of the Prophets, the Orb of Prophecy and Change, which induces a vision of his past, when he first met his wife.

Nine of these 'orbs' have been found in Bajoran history, but eight have been stolen by the Cardassians. Kai Opaka fears that the Cardassians will seek out the Celestial Temple, the home of the Prophets, in order to control their power. She cannot help him to unite Bajor, she tells him, until the prophets have been warned of this danger. She gives him the orb, and he returns with it to DS9, where he sets Jadzia the task of finding the Celestial Temple. She, too, has a vision, of her joining with the Dax symbiont.

Dax discovers a pattern which suggests the Celestial Temple might be located nearby, and when they approach its approximate location, they are pulled through a wormhole to the Gamma Quadrant. On returning through the wormhole, though, their runabout slows and seems to land inside the wormhole. Shortly thereafter, Jadzia is sent from the wormhole toward DS9, while Sisko remains trapped inside. Recognizing the value of a stable wormhole, Kira orders DS9 moved closer to it.

Inside the wormhole, Sisko is shown scenes from his memories, but the other people in his memories talk to him. He realizes that these are aliens that live inside the wormhole: Bajor's Prophets. It becomes clear that the aliens are not corporeal and do not experience time in a linear fashion, and they are concerned that Sisko means to destroy them. Sisko spends a while trying to convince them otherwise and to explain the meaning of a linear existence, and in the process realizes that his existence isn't quite as linear as he believed: that he has never really left the time when his wife died.

Ultimately, Sisko succeeds in convincing the aliens to allow passage through the wormhole, and returns to DS9, resolved to command the station, rather than return to Earth, as he had been considering.