Doubt

Set in 1964 at a Catholic church in the Bronx, New York, the film opens with Father Flynn (Phillip Seymour Hoffman) giving a sermon on the nature of doubt, noting that, like faith, it can be a unifying force. The next evening, Sister Aloysius (Meryl Streep), the strict principal of the attached school, discusses the sermon with her fellow nuns, the Sisters of Charity of New York. She asks if anyone has observed unusual behavior to give Father Flynn cause for preaching about doubt, and instructs them to keep their eyes open for any such behavior.

Sister James (Amy Adams), a young and naive teacher, observes the closeness between Father Flynn and Donald Miller, the school's only African-American student and an altar boy. One day during class, Sister James receives a call in her class asking for Donald Miller to meet Father Flynn in the rectory. When he returns, Donald is distraught and Sister James notices the smell of an alcoholic drink on his breath. Later, while her students are learning a dance, she sees Father Flynn placing a white shirt in Donald's locker. On guard for unusual behavior, Sister James reveals her suspicions to Sister Aloysius.

Under the pretext of discussing problems with the school's Christmas play, Sisters Aloysius and James confront Father Flynn with their suspicions that his relationship with Donald may be inappropriate. Several times Father Flynn asks them to leave the matter alone as a private issue between the boy and himself but Sister Aloysius persists. The priest reveals that Donald had been caught drinking altar wine. Father Flynn explains that he had promised Donald not to tell anyone about the incident, and that he could remain an altar boy. Having now been forced to break that promise and reveal the truth, he will need to dismiss Donald as an altar boy. Father Flynn tells Sister Aloysius that he is displeased in the way she handled this.

Initially, Sister James is relieved and convinced of Father Flynn's innocence, but Sister Aloysius' belief that he has behaved inappropriately with the boy is unshakable. Sister James later confronts Father Flynn about the shirt she saw him leaving in Donald's locker, having not revealed this detail to Sister Aloysius. They discuss his relationship with the boy. Father Flynn reveals a reasonable explanation for the situation and Sister James' doubts are assuaged.

Sister Aloysius sends for Donald Miller's mother to reveal her suspicions. Mrs. Miller (Viola Davis) shocks Sister Aloysius by stating that she should not pursue the matter further and that he only has to last until the end of the school year before he goes on to attend high school. She also hints at Donald's homosexuality and reveals that he has a physically abusive father. She begs Sister Aloysius to drop the matter, and rationalizes Donald's relationship with Father Flynn to protect him from his father, and because his chances of going to a better high school would increase after finishing from a prestigious church school.

Despite having no evidence and no support from Donald's mother, Sister Aloysius in their final showdown demands that Father Flynn tell the truth or she will go to his superiors. Father Flynn repeats that there is no illicit relationship, but Sister Aloysius says she knows that he has a history of problems, having moved to three different parishes in five years. She tells him that she has contacted a nun at one of his prior churches (she refuses to say whom) and that this nun corroborated her suspicions. Father Flynn is furious that she has contacted a nun rather than the church's pastor; the latter being the proper church protocol. Sister Aloysius demands that he resign. Unable to stand up to her willingness to destroy his reputation, he succumbs to her demands.

Following his final sermon, the nuns sit together in the church garden. Sister Aloysius tells Sister James that although Father Flynn has left, he has been promoted from assistant pastor to that of pastor at a different church and its parochial school, in effect a promotion. She goes on to reveal that she lied about speaking to a nun at Father Flynn's former church, and thus never found hard evidence against him. Repeating a line from earlier in the film that "in the pursuit of wrongdoing, one steps away from God."

Sister Aloysius concludes that one also pays a price in pursuing wrongdoing. She breaks down in tears and reveals to Sister James "I have such doubts." The viewer is left to determine on their own whether Father Flynn was guilty or innocent of misconduct.