Long ago, a tablet prophesying the Reckoning was kept below the city of B'hala. The Reckoning itself had long been forgotten by Bajoran scholars. The tablet remained hidden for 30,000 years, until 2374 when archaeological digs at B'hala uncovered it, and invited the Emissary of the Prophets, Starfleet Captain Benjamin Sisko to come see it. Ranjen Koral gave Captain Sisko, his son Jake and Major Kira Nerys a brief tour of their progress excavating the city before showing him the tablet – which foretold his arrival, the only decipherable ideograms reading "Welcome, Emissary."
It started with an instability of the Bajoran wormhole, which caused floods, earthquakes and storms on Bajor. It eventually turned out to be a showdown between the Prophets and the Pah-wraith (or "Kosst Amojan") at the "Gateway to the Celestial Temple." For the battle, the Prophets took possession of Major Kira's body, the Pah-wraith of Jake Sisko's. The battle ended without a decision when Kai Winn flooded the promenade with chroniton particles, forcing both entities to leave the station. (DS9: "The Reckoning")
During a flashback in the novel Q-Strike, reference is made to a moment in Bajor's past when the Bajorans believed that the Reckoning had come when they witnessed lights in the sky, but this was actually the result of the being known as Gorgan attempting to escape the female Q by fleeing down the Bajoran wormhole only to be expelled by the Prophets.