Bajor is about to elect a new spiritual leader, and Kira's lover, Vedek Bareil, is the leading candidate, having been Kai Opaka's personal choice to succeed her. After spending time with Kira on the station, Bareil prepares to return to Bajor, but the two of them first come across Vedek Winn, who is running against Bareil for Kai. Kira can barely contain her anger toward Winn, as she still blames her for an attempt made on Bareil's life. After this confrontation, Kubus, an older Bajoran, attempts to come onto the station unnoticed, but is spotted by another Bajoran, who recognizes him as a known Cardassian collaborator. As a crowd gathers, Odo arrives and arrests Kubus, while an inconspicuous Winn watches the entire scene.

From his cell, Kubus tells Odo and Kira that he wants to return to Bajor, where he can live out his last years, but Kira insists he remain in exile. Later, however, she learns that Vedek Winn has met privately with Kubus and now plans to take him back to Bajor. Kira stops her ship from leaving, then finds out that Winn has been investigating the Kendra Valley Massacre, in which 43 Bajoran freedom fighters, including Kai Opaka's son, were killed by the Cardassians. A Bajoran monk, Prylar Bek, admitted to betraying the group's location before committing suicide. Winn then reveals to Kira that she has given Kubus sanctuary in exchange for information about the massacre — information that implicates Vedek Bareil as the collaborator who ordered Bek to reveal the location.

Winn offers Kira the chance to prove Bareil innocent before the accusations become public. Kira questions Kubus, who reveals Bek saw Bareil just after the massacre, then killed himself. Bareil later claims to Kira that he only counseled the troubled monk. Odo then makes a disturbing discovery. The communications records between Bek and the Vedek Assembly for the week leading up to the massacre have been sealed — an act which only a Vedek, like Bareil, could perform.

Kira and Odo find Quark and convince him to bypass the seal for them. When he does, he finds that all transmission records have been erased. O'Brien attempts to learn who did this by searching for fragments of the responsible party's retinal scan and cross-referencing the data with the Assembly archives. Kira's worst fears are realized when O'Brien's search identifies Vedek Bareil.

Kira goes to Bajor and confronts Bareil with what she has learned, and he admits that Bek was ordered to reveal the location of the Kendra Valley resistance fighters to prevent the Cardassians from wiping out every village in the area in search of them — a scenario in which more than a thousand Bajorans would have died instead of 43. Feeling betrayed, Kira is unable to forgive Bareil. Later, she reluctantly contacts Winn, who says that Bareil has withdrawn from the election. Certain that he is too honorable to cover up his own misdeeds, Kira investigates further. After Winn becomes the new Kai, Kira again finds Bareil and presents proof that he did not give Bek the order, then tells him that she has figured out the truth. All this time, Bareil was covering for the real collaborator — Kai Opaka, who sacrificed her son to save the Bajoran villagers. Bareil kept Opaka's secret, but at the cost of handing the spiritual leadership of Bajor to Winn.