Sisko is called to Bajor when an ancient tablet addressing the Emissary is discovered. Seeing the tablet, Sisko launches into a vision, during which the Prophets tell him "The Reckoning" must begin. Since no one knows exactly what this means, Sisko takes the tablet back to Deep Space Nine for Dax to translate. Kai Winn arrives on the station and pushes Sisko to return it, but he refuses, convinced he is doing the will of the Prophets.

Soon afterward, the wormhole begins opening and closing. When the Kai informs Sisko that Bajor is suffering floods and tornadoes and accuses him of angering the Prophets, Sisko agrees to return the tablet on the next morning's transport. Later that night, Sisko examines the tablet one final time. He instinctively smashes it on the ground, releasing a strange vortex of violent energy.

Sisko tells Winn he believes he has done what the Prophets wanted him to do. While privately moved, she refuses to acknowledge Sisko's faith in her gods and continues to blame him for the destruction affecting Bajor. In the midst of Winn's ranting, Sisko is called to the Promenade, where Kira is ablaze with bluish energy. He realizes that she is no longer Kira, but a Prophet announcing it is time for the Reckoning.

The Kira/Prophet reveals she is to fight an epic battle with an Evil One, a Pah-wraith banished from Bajor's celestial temple. Winn is thrilled — according to prophecy, the defeat of the Evil One will usher in Bajor's Golden Age. Feeling he has no choice but to allow the battle, Sisko orders the station evacuated. Dax and Bashir rig a panel with radiation that will force the Prophet to leave Kira's body, but Sisko insists the showdown proceed without interference. He stands by his decision even when the Pah-wraith takes over the body of his son, Jake.

Sisko watches helplessly as both Jake and Kira are wracked by the conflict. Dax suggests using the radiation, but Sisko refuses, believing that the Prophets will protect his son. When the Kai sneaks away and triggers the radiation, she ends the battle before one of the combatants is defeated. Later, Kira escorts her off the station and is shocked to hear the religious leader praising herself for saving Deep Space Nine. Kira answers her with a conviction she has never known before, telling Winn she has defied the Prophets so completely that even they may not know what it means for Bajor.