The first act of Doubt consists of a sermon by Father Flynn. His theme is uncertainty, which he relates to the disorientation felt by most of the country the year before, when President John F. Kennedy was assassinated. He points out how people came together spiritually and concludes that despair does not have to be an experience that isolates people, if they have faith. To make his point, Father Flynn tells a story about a sailor, lost at sea, who uses his memory of the stars to guide his navigation, even when the stars are covered by clouds for more than twenty nights. The sailor's faith in the truth he once knew is likened to the despairing person's faith in God.
Sister Aloysius, the principal of St. Nicholas School, meets in her office with Sister James, who teaches eighth grade. She asks about a boy who has been sent home with a bleeding nose and warns that children sometimes inflict their own injuries as a way to leave school. During the conversation, Sister Aloysius reveals her dislike of teachers who act kind in order to hide their own weakness or laziness.
The talk turns to whether Sister James stays in the room when the "specialty" instructors—those in charge of teaching art, music, physical education, and similar subjects—come in. In particular, Sister Aloysius is interested in whether Sister James leaves the boys alone when Father Flynn teaches religion and physical education. She asks Sister James to be alert, but she cannot find it in herself to be more specific about what she suspects.
Act 3 comprises another monologue by Father Flynn, addressing the boys during basketball. He tells them that they will be able to shoot better if they relax and quit thinking about how they might look. On the subject of personal hygiene, he tells an apocryphal story about a boy with whom he grew up, named Timmy Mathisson, who had dirty fingernails that he put in his nose and in his mouth, which resulted in his death from spinal meningitis.
Sister Aloysius and Sister James meet in the garden. Sister James explains that the boys in her class are at a lecture, given by Father Flynn, on the subject of being a man. Sister James explains that the new African American boy in her class, Donald Muller, does not have to worry much about bullying from the other students, because Father Flynn has taken on a role as his special protector. Immediately, Sister Aloysius says that she thinks Father Flynn is planning inappropriate behavior with the vulnerable boy. Sister James recalls that Father Flynn took Donald for a private talk to the rectory and that, when he came back, Donald had alcohol on his breath.
Sister Aloysius explains that it would be difficult to have a priest removed, even if there was evidence that he had had sex with a student. Father Flynn would certainly deny any such allegation, and Monsignor Benedict would believe whatever Father Flynn said. The rules of the Church prohibit a nun from taking suspicions to any higher authority. The boy would not talk, intimidated by shame....
(The entire section is 1295 words.)