In a Bronx Catholic church, a year after Kennedy’s assassination, recently arrived Father Flynn (Philip Seymour Hoffman) gives a sermon about doubt. Sister Aloysius (Meryl Streep), principal of the church’s school, is intrigued by the sermon’s origin, because it comes from somewhere, and she suggests to her fellow Sisters of Charity to keep an eye out for anything suspicious.
Sister James (Amy Adams) notices a seemingly unusual closeness between Father Flynn and Donald Miller, an altar boy and the school’s only black student. During her class, Donald is called to the rectory to meet Father Flynn. Upon his return, Donald appears bothered, and she notices alcohol on his breath. Later, she witnesses Father Flynn place a shirt in Donald’s locker, and reports what see has seen to Sister Aloysius, who is troubled because she has seen inappropriate relations between priests and boys before in the Church.
Under the guise of discussing the Christmas pageant, Sister Aloysius, with Sister James recounting what she witnessed, confronts Father Flynn, who doesn’t wish to discuss the matter. Feeling this confirms his guilt, Sister Aloysius continues to press until he reveals Donald was caught drinking sacramental wine and was dealing with it privately. However now that it had come out, Donald would lose the privilege of being an altar boy. Sister James is relieved and accepts Father Flynn’s explanation. Sister Aloysius refuses to believe him, trusting her own certainty on the matter.
After Donald’s mother (Viola Davis) visits with Sister Aloysius, Father Flynn demands she stop her witch-hunt. She refuses, stating she is willing to sacrifice everything to see justice done. She wants his confession, but he repeats there’s nothing to confess. Although admitting he has sinned, Father Flynn never admits to Sister Aloysius’ charges and Shanley never gives us any proof, leaving the viewer only with Sister Aloysius’ certainty.
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