It's 1964, St. Nicholas in the Bronx. A charismatic priest, Father Flynn, is trying to up-end the school's strict customs, which have long been fiercely guarded by Sister Aloysius Beauvier, the iron-gloved principal who believes in the power of fear and discipline. When Father Flynn pays too much attention to a new student, Sister Aloysius sets off on a personal crusade to unearth the truth and to expunge Flynn from the school.