In a strict Catholic school in New York in 1964, the lives of students and teachers are shaken by the emergence of a troubling suspicion. Sister Aloysius Beauvier, a strong-willed woman with firm convictions, becomes the voice of doubt when she begins to suspect that the charismatic Father Flynn, a beloved priest among the students, is abusing a student. Aloysius, with her rigid approach and aversion to modernity, decides to take matters into her own hands and embarks on a mission to unmask what she considers a grave injustice and a betrayal of the community's trust.
However, things are not that simple. As Aloysius delves deeper into her investigation, she faces resistance from Father Flynn himself, who defends his innocence and the importance of compassion and understanding in education. The tension between the two escalates, leading to a moral confrontation that questions the nature of truth and authority.
Sister James, a young teacher who admires Flynn, finds herself caught in the middle of this conflict, becoming a pawn in the power and conviction struggle unfolding between her superiors. With each revelation, the film challenges perceptions of justice and righteousness, taking the characters and the audience to a crossroads where doubt becomes the only certainty. Some decisions can change everything, even when the truth seems unattainable.