It's 1964 St. Nicholas in the Bronx. A charismatic priest Father Flynn is trying to upend 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-based discipline. The winds of political change are sweeping through the community and indeed the school has just accepted its first black student Donald Miller. But when Sister James a hopeful innocent shares with Sister Aloysius her guilt-inducing suspicion that Father Flynn is paying too much personal attention to Donald Sister Aloysius sets off on a personal crusade to unearth the truth and to expunge Flynn from the school. Now without a shard of proof besides her moral certainty Sister Aloysius locks into a battle of wills with Father Flynn which threatens to tear apart the community with irrevocable consequences.