O'Brien, working with his young Bajoran apprentice, Neela, is concerned when he cannot locate one of his tools, one which can be used to access every critical system on the station. When it turns out Ensign Aquino is also missing, they make a search, finding the melted remains of the instrument in a large power conduit — plus traces of organic material, which prove to be human remains. Apparently, Aquino went to fix an irregularity in the conduit, and accidentally got caught in the power flow and killed. Later, O'Brien and Keiko find to their dismay that some Bajorans are treating her with contempt. In front of the school, the O'Briens find Bajoran parents and the students, including Jake, listening to Winn, who asks Keiko to stop teaching about the wormhole altogether if she will not instruct the children about the spiritual aspects. When Keiko refuses, Winn leads away the Bajorans in silent protest. O'Brien comforts his saddened wife.

O'Brien is still puzzled by Aquino's death, and Sisko asks Odo to investigate further. Jake then approaches his father about the school situation, and Sisko explains to him the importance of respecting the beliefs of others. Realizing the growing uneasiness on the station, Sisko seeks help on Bajor from Vedek Bareil, a spiritual leader who is the leading candidate to become the planet's next Kai. Although his ideology is quite different than Winn's, Bareil will not risk his growing status to help Sisko get an audience with the Vedek Assembly. Frustrated, Sisko returns to the station and finds that three Bajoran crewmembers failed to report for duty due to "illness," according to Kira. Tension builds between the two as Sisko grows tired of these games, but Odo and Bashir interject with the results of their investigation — Aquino was really killed by a phaser blast.

The officers discuss the murder, and Odo reveals that, according to turbolift records, the ensign's true destination that fateful night was Runabout pad C. While O'Brien and Neela investigate the area, Odo goes to the Promenade just as more Bajorans, members of an orthodox spiritual order, arrive on the station to support Winn. O'Brien finds Odo and reports something most unusual — a security bypass module was placed at Runabout pad A. Odo deduces that Aquino must have interrupted someone planning to steal a Runabout from pad C. The ensign was killed, and the culprit went to pad A to escape later detection. Odo and O'Brien suddenly hear an explosion, and rush to find Keiko's school engulfed in flames.

The wreckage is examined, revealing the school was destroyed by a homemade bomb. Winn approaches the area, and an angry Sisko lets her know that, despite this terrorist act, the majority of Bajorans do not feel the contempt she does for the Federation. As he leaves, Winn is surrounded by her supporters, and silently acknowledges Neela in the crowd. Then, in the Bajoran shrine, Neela reveals privately to Winn that the officers know about the Runabout, leaving Neela with no mode of escape, but Winn insists their secret plan must be carried out — it is "the will of the prophets." Later, Sisko is pleased as Bareil arrives at the station to survey the situation, and while they move through the huge crowd of Bajoran well-wishers with Kira, O'Brien finds an unknown file in the computer, which turns out to be a series of forcefield overrides to Runabout pad A — an escape route from the Promenade. While Bareil and Winn together go to the remains of the school, O'Brien suspects the weapons detectors are disabled, and urgently tells Sisko only Neela — the last person to repair that unit — could have done it. Sisko spots Neela in the crowd, calmly pulling out a phaser, and he knocks her to the ground, making Neela miss her target — Bareil. It is discovered Winn started the religious controversy as a ruse to have Bareil assassinated before he could be made Kai. But in the end, it only serves to strengthen the alliance between Sisko and Kira.