John Patrick Shanley's play, Doubt, was formally titled Doubt: A Parable, when it was originally produced for the stage. The use of "parable" as a sort of subtitle is a clever play on words, as it refers to a brief story that illustrates a moral lesson, as is done throughout the New Testament (Jesus' parables used to instruct followers). Given the subject matter of Doubt, it is an apt use of the word, and particularly inventive given both the theme and the main title ("Doubt").
Doubt is the story of a senior nun and parish school principal, Sister Aloysius, and her conflict over whether and how to confront the parish priest, Father Flynn, with allegations of sexual misconduct. Sister Aloysius' approach to discipline and learning is at strong variance with the philosophy of Father Flynn, so there is already tension in the relationship before the priest is accused of sexually molesting a boy. As the story progresses, the title of the play assumes more meaning. Initially, Father Flynn's sermon on "doubt" with regard to allegiance to the gospel establishes the setting for the conflict between him and Sister Aloysius, the former being more liberal and the latter strictly conservative. "Doubt" begins to assume greater meaning with regard to the suspicions surrounding the priest and whether he is guilty of sexual misconduct. In the end, nothing is resolved.
The theme of Shanley's play Doubt is in fact the nature and importance of doubt. Sister Aloysius believes that Father Flynn is having an inappropriate relationship with Donald Muller, an African American student at the Bronx Catholic school where they work. At the end of the play, Father Flynn is transferred to another Catholic school, and Sister Aloysius never figures out definitively whether Father Flynn had an inappropriate relationship with Donald Muller or not. She is left only with doubts.
Sister James, a young and innocent nun, says at one point during the play, "But it's so unsettling to look at things and people with suspicion. It feels as if I'm less close to God." While Sister James and Sister Aloysius desire certainty in their lives, in reality life is not conducive to certainty. Instead there are moments of doubt, and one can't always be sure of the truth. Doubt plays a role in both religion (in which one is always tempted to be skeptical in the face of faith) and in life. Doubt is a healthy response to the uncertainties of life, and the alternative is to condemn others without proof.