At their regular staff meeting, the crew of Deep Space 9 review the state of the Dominion War. It is a time of great uncertainty as the threat of a Dominion attack on Vulcan looms overhead, and while the Romulans have retaken Benzar (home to the Benzites), there is no way to be certain they will relinquish control after the war. For now, Sisko, Kira and Jake are taking a trip to Bajor to visit a new discovery in the remains of B'hala. Although Dax observes how trivial such things seem in the midst of a war, but the archaeologists have specifically requested Sisko's presence.
Ranjen Koral leads the trio through the ruins, where numerous tunnels have been dug and excavations have taken place since Sisko's last visit. Jake seems bored but puts up with it for his father's sake. The monk leads them to a pedastal with some "interesting" writing in Ancient Bajoran; part of the text reads, "Welcome Emissary". As he touches it, he is thrown across the room. He loses consciousness as the Prophets send him a vision in which they mention the end and the beginning and claim that "the reckoning" is at hand. As usual, they do not state their intentions directly, but something important is about to happen.
Sisko takes the tablet back to DS9, where he and Dax study it in a science lab to confirm what Dax suspected from the beginning; it is a slab of stone with nothing unusual about it. Though she is less than enthusiastic about the task, he asks her to translate the words on the tablet. In the meantime, he greets Kai Winn at the airlock. She is visibly troubled by the removal of the tablet from Bajor. In her usual, subtle manner, she compares his actions to the plundering the Cardassians did during the Occupation. The Emissary's belief that the Prophets wanted him to bring the tablet to DS9 nonetheless seems to satisfy her for the moment.
Shortly thereafter, Sisko learns that nothing could be further from the truth. Winn lodges a formal complaint with Starfleet Command, and Admiral Ross tells Sisko to stop meddling in Bajoran affairs. Despte this, Sisko remains convinced that the tablet is the key to something important. Unfortunately, when Dax discovers the meaning of the words, she finds the tablet says that, among other things, the Prophets will weep and the gateway to the Celestial Temple - DS9 - will burn.
We now find Dr. Bashir, Odo, and Worf siting idly on the second level of Quark's, considering the repercussions. As Quark himself walks by, he complains about how bad business has been because of talk about the "reckoning," but their conversation is cut short as the station is rocked by a shift from the nearby wormhole shifts again. Meanwhile, Sisko and Winn have met in his office, where she informs him of flooding, earthquakes and the like taking place on Bajor as they speak. She believes he has angered the Prophets by taking the tablet, and she has a request from First Minister Shakaar stating as much. With no other choice, Sisko agrees to return the tablet in the morning.
Although Dax has made progress in her translation of the tablet, she is unsure of what exactly it is foretelling; she thinks it says the Bajoran people will either eat fruit or suffer horribly. Kira is suspicious of Winn's motives as usual, but more than anything Jake is worried about his father, particularly the vision of Opaka. After nearly losing his father during a period of similar visions, Jake is scared.
That night, Sisko is unable to sleep and finally heads for the science lab. He mulls over the tablet for a while before becoming frustrated with the obscure nature of the Prophets' warnings and smashing it. As he looks down at its shattered remains, some form of red-and-blue energy discharge comes from it and seems to disappear through the ceiling. Dax and Odo find no signs of such a discharge, although there is an unexplained energy drain. What's more, Winn believes Sisko smashed the tablet just to spite her. As he tries to reassure her that the Prophets have a plan and wanted him to smash the tablet, he is called to the promenade.
Sisko finds Kira standing in the doorway to the Bajoran temple with electricity or some other phenomenon emanating from her hands. Her body has been inhabited by one of the Prophets, so he tells the security personnel to lower their weapons. Although they are worried for Kira's safety, Odo reassures Sisko that Kira would have been willing to surrender herself to the Prophets no matter what the consequences, even if it meant her death. The Prophet approaches Sisko to announce that "the reckoning", which will be either the end or the beginning, has begun and she awaits the Evil One, Kosst Amojan. Winn recognizes the Prophet's words, as the beginning to which she referred is the prophecied 1,000-year Golden Age of Bajor. She offers herself to the Prophet as its humble servant but is ignored; the Prophet simply informs Sisko that his task is complete.
Knowing something disastrous may happen to the station, Sisko begins an evacuation. However, Dax and Worf are not sure it is necessary to do so. She suggests that they slowly but gradually flood the promenade with chroniton particles, which are fatal to the Prophets, which would force it to leave. Given what the Prophets have done for him and Bajor, Sisko refuses. Even the Federation owes the Prophets enough to let it play out after that destroyed a fleet of Dominion ships to save DS9.
Worf and Odo find one another near the airlock as they oversee the evacuation of the civilian population. Worf admires Odo's devotion after what Odo said about Kira letting the Prophet take her, and he is unsure that he could have done the same if it had been Jadzia. With Kira on their side, Odo assures Worf the Prophets will be victorious.
Meanwhile a group of Bajorans, led by Winn, refuses to leave the promenade as they pray for the Prophets' victory. Sisko confronts Winn and threatens to personally order the people to leave as their Emissary. She has her "children" leave and it is obvious she is jealous of Sisko's role. Their conversation is interrupted when the Prophet announces that Kosst Amojan has chosen his vessel; Jake Sisko emerges on the second level and claims it is time for the reckoning to begin. Despite Sisko's protests and pleas to take him instead, the pah-wraith waves its hand, throwing Sisko across the room.
Kira and Jake face off and energy beams of some sort, red from Jake and blue from Kira, come out of their chests and meet at the center. The spectacle continues as sparks fly and the energy buildup reaches critical levels. As the buildup could trigger an explosion at any second, Dax and Winn in an unusual state of agreement urge Sisko to leave the station; however, he is determined to stay and see the reckoning through. The others decide they must evacuate the station, leaving it abandoned save for Sisko, Winn, Jake, and Kira. While Dax hurries to ensure that everyone is evacuated, Winn sneaks away and heads to Ops, where she reluctantly approaches a computer console. With tears in her eyes, she triggers the chroniton increase. "May the Prophets forgive me," she whispers.
The veins on Jake's face have popped out in the meantime as the Prophet appears to be winning the celestial battle. When the chroniton levels begin to rise, the Prophet screams out in protest, but both spirits are forced to leave the station, causing both Kira and Jake to collapse.
Sisko visits his son in the infirmary, where Jake is still weak but will recover eventually. He tries but does not know what to say to his son to explain the incident, but no explanation is necessary. Jake was able to feel the Pah-wraith's hatred and knew it had to be destroyed, even if it meant his death.
As Odo and Kira walk together on the promenade, she thanks him for his confidence in her and willingness to let her go if the Prophet's victory meant her death. His ability to let her die for her faith is flattering, although he reassures her that he still would have been happier if the Prophets had chosen someone else. Kira then escorts Kai Winn to the airlock, where Winn claims Sisko should be grateful for her actions. Kira knows Winn's true motive was not the good of Bajor but her jealousy of Sisko, and thanks to Winn, the evil of Kosst Amojan still exists. Because of her, the future of Bajor, DS9, and everything else is uncertain.