Vedek Fala, a Bajoran monk and Kira's former teacher, pays her an unexpected visit. He gives Kira a crystal which transports her to Empok Nor, where, to her horror, she is met by her old enemy Dukat — a Cardassian who oversaw the occupation of Bajor. He is now the leader of a Bajoran religious faction which worships the Pah-wraiths — the corporeal enemies of Bajor's Prophets. Dukat wants Kira to join his followers on the abandoned Cardassian space station.

Although Kira is suspicious of Dukat's motives, Pah-wraith convert Fala tries to convince her that the Cardassian has changed. While being held against her will, Kira meets Dukat followers Mika and Benyan, a Bajoran couple who were granted his permission to have the first baby on Empok Nor. The community's devotion to Dukat becomes clear when Kira takes aim at him with a stolen phaser, and residents shield him with their bodies, then knock her unconscious.

When Kira regains consciousness, she confronts Dukat about his long affair with her mother during the Bajoran occupation, and is stunned when he expresses regret. Their conversation is cut short by word that Mika is in labor. To everyone's surprise, Mika's baby is half-Bajoran and half-Cardassian. Dukat proclaims that the infant is a miraculous, living symbol of his covenant with the Bajoran people, though Kira is certain Dukat fathered the child.

While Kira questions Fala and Benyan about the baby's paternity, Dukat meets with Mika, who fears she won't be able to keep the explosive secret that they slept together. Desperate to cover his tracks, Dukat sets up an "accident" which nearly claims Mika's life. Kira saves her, and in front of Dukat's followers, accuses him of impregnating Mika. In response, Dukat announces that the Pah-wraiths want the group to join them — by committing mass suicide.

Kira is locked in a room while Dukat proceeds to the temple, where his followers are ready to ingest poisonous capsules. Kira escapes, interrupts the deadly ceremony and exposes Dukat as a fraud who never intended to kill himself. After Dukat flees, a disillusioned Fala takes a fatal capsule, and the Defiant arrives to rescue Kira and the other remaining followers.