The episode begins in the wake of the Cardassian withdrawl from Bajor, after an occupation of some decades. While the Cardassians have sabotagued most of the Bajoran infrastructure, they left a mostly-working space station in orbit; which the Bajorans have requested Starfleet help in running.
Commander Benjamin Sisko arrives at the station; persuades the Ferengi bartender and 'community leader' Quark to stay; and starts to investigate the mystery of the 'orbs', or the 'Tears of the Prophets'. Sisko is proclaimed the 'Emissary', a figure in Bajoran religion. They track the source of these to a previously undiscovered wormhole in the Bajoran system, and investigate. They discover what may be the Bajoran prophets, called by the Starfleeters, the 'wormhole aliens', living within the wormhole, and discover that it links to the Gamma Quadrant.
The Cardassians, annoyed that this should happen barely days after they withdrew, arrive to claim the wormhole for themselves, but are foiled. The station is relocated to very close to the wormhole.