Benedetta’s stigmata are revealed to be partially aided by physical means; during high-stress trances, she uses shards of broken pottery to cut her hands, feet, and forehead, mirroring the wounds of Christ. However, her trances and male-voiced prophetic proclamations appear genuinely uncalculated, leaving her exact psychological state ambiguous.
Sister Christina secretly observes Benedetta cutting herself and reports the fraud to the Abbess. When church officials side with Benedetta's popular acclaim and elevate her to Abbess, Christina is forced into public penance and eventually leaps to her death from the convent tower.
Displaced Abbess Felicita discovers the carved Virgin Mary sex toy hidden in Benedetta's cell and travels to Florence to alert the Papal Nuncio. The Nuncio arrives in Pescia, arrests Benedetta and Bartolomea, and subjects Bartolomea to genital torture on the strappado, coercing a confession regarding their sexual relationship.
Sentenced to be burned at the stake, Benedetta is tied to the pyre. Sister Felicita, overwhelmed by guilt over the cruelty of the Nuncio and his men, throws herself onto the flames. Benedetta uses the gathered crowd's hysteria, her divine claims, and the encroaching terror of the plague to incite a mass riot against the Nuncio. The Nuncio is killed by the mob and exposed to plague infection.
In the aftermath of the riot, Bartolomea and Benedetta escape the city walls. While Bartolomea urges Benedetta to flee to the countryside and live in secular freedom, Benedetta chooses to turn around and walk back into the plague-ridden convent in Pescia, accepting that her true arena of power and identity exists only within the walls of the cloister.