An archeological dig on Bajor reveals an ancient tablet in an ancient Bajoran language that addresses the Emissary. Captain Sisko opts to bring the tablet to Deep Space Nine to allow the computers there to help examine further, but this raises the ire of Kai Winn, who believes the tablet must remain on Bajor. As Sisko studies the tablet, which speaks of an upcoming battle called the "Reckoning", he is suddenly compelled to smash it open, releasing red and blue vapors that dissipate into the station. Kai Winn arrives at the station, furious that Sisko broke the tablet, but Sisko reveals that he believes he was meant to do that.
The staff of the station discover numerous power fluctuations they cannot identify. They soon discover that Major Kira Nerys has become possessed by the blue mist, discharging massive amounts of energy through the Promenade. While Sisko orders the station's staff to see what can be done, he learns that the blue mist is one of the Bajoran Prophets, willingly taken in by Nerys to prepare for the Reckoning, and that a Pah Wraith will be seeking its own host to join in battle. The staff discovers that they could flood the Promenade with radiation to force the being to leave Nerys, but Sisko orders them to hold off, believing the confrontation to be necessary. The Pah Wraith reveals himself to have taken over the body of Jake Sisko, and the two begin to face off on the Promenade, creating a dangerous energy buildup. Sisko orders a full station evacuation, including the senior staff, but refuses to leave his son behind. Kai Winn, who managed to avoid the evacuation, executes the command to flood the Promenade with radiation, excising the spirits but leaving the hosts physically stressed. After her recovery, Nerys states to the Kai that she had stopped the Reckoning, and that the consequences of that will rest on her shoulders.