Act I

Scene one – St. Nicholas Church 

Father Flynn preaches a sermon on the subject of doubt and its relationship to a crisis of faith in the wake of recent cataclysmic world events.

Scene two – a classroom in the St. Nicholas School 

Sister James, a young nun, teaches history to her class. Sister Aloysius, the school principal, observes with scrutiny. She confiscates a barrette from one student and a transistor radio from another.

Scene three – the convent dining room 

As the nuns eat a modest dinner, Sister Aloysius reviews the Sunday sermon. She advises all the sisters to be on alert for a potential problem.

Scene four – the garden

The aged Monsignor Benedict and Father Flynn walk outside, discussing their dinner the night before. The monsignor expresses his confidence in the younger priest.

Scene five – the classroom 

Sister Aloysius encounters Sister James in her empty classroom. The teacher inquires after a student, William London, who was sent home. It is revealed that his nosebleed was probably self-induced, and Sister Aloysius chides Sister James for being too naïve. The younger nun prefers to handle problems herself, but Sister Aloysius outlines the chain of discipline.

Looking out the window, Sister Aloysius sees Father Flynn with Donald Miller, the school’s first African-American student. She reacts uneasily.

Scene six – the school basement 

Father Flynn coaches a game of basketball with the students. 

Scene seven – montage 

Scene eight – the school gym 

As Sister James observes a dance class, she see Father Flynn put something in a locker. Investigating further, she finds a white tee shirt. Donald then enters the gym, looking troubled.

Scene nine – the garden

Sister James encounters Sister Aloysius, who asks for an update. The girls of her class are studying music, while the boys are in the rectory getting a talk from Father Flynn. They discuss Donald. Sister Aloysius fears he may be a target of bullying, but Sister James reassures her that he has a protector in Father Flynn. The older nun becomes tense. Sister James confesses her uneasiness since their last conversation, but Sister Aloysius reassures her that righting a wrong is God’s work.

Sister James begrudgingly reveals her suspicions, recalling the incident during dance class. Donald seemed somewhat unsettled after being called to the rectory for a talk with Father Flynn, and she detected liquor on his breath. Sister Aloysius suspects an abusive situation, but her hands are tied by the Church. Her only recourse is to report the allegations to the monsignor, who would likely suppress the matter after hearing Father Flynn’s denial. She plans to confront the priest directly, and protocol demands someone else to be present in the room, namely Sister James. The young nun is clearly uncomfortable at this prospect

Scene ten – the conference room 

Father Flynn arrives at the conference room as appointed. The meeting is being held under the guise of planning the Christmas pageant. The concern of Donald Miller’s role comes up and any special attention in the drama due to his race. Sister Aloysius segues the conversation to the subject of his visit to the rectory, and Father Flynn realizes something is afoot. He is indignant over her tone and refuses to discuss the matter further.

He is about to leave the room when Sister Aloysius reveals that Donald had smelled of alcohol. The priest explains – Donald was caught drinking the altar wine in the sacristy. Flynn took pity on him, promising to keep the incident a secret so he wouldn’t be removed from the altar boys. He leaves, disturbed by the meeting. Sister James is reassured, but Sister Aloysius is convinced he is lying and is determined to bring him down.

Act II

Scene one – the church 

From the pulpit, Father Flynn relays a parable about idle gossip and the harmful consequences of bearing false witness against one’s neighbor.

Scene two – the garden

Father Flynn encounters Sister James outside. They discuss his sermon and the unspoken accusations against him. The young nun has only been following the directions of her superior, but asks him directly if the assertions are true. Flynn continues to deny everything. He claims he was only reaching out to the boy, showing him the compassion the cold-hearted nun refuses to give to others. He encourages Sister James not to lose her humanity.

Scene three – the principal’s office 

Sister Aloysius has called Donald’s mother to her office. Mrs. Miller reports that her son is upset over being removed from the altar boys, but had admitted to drinking the wine. She hopes this incident won’t ruin his future at the school, for he only needs to make it until June, after which he will be off to high school, and hopefully, college. Sister Aloysius bluntly declares her suspicions about Father Flynn, and believes he gave Donald the wine. Mrs. Miller comes to realize she is willing to let the potentially improper relationship continue rather than cause more trouble for her sensitive son, who is hated and abused by his  father – it will only be for a few more months.

Scene four – the principal’s office 

After Mrs. Miller leaves, Father Flynn storms into the room, having spotted her. He confronts Sister Aloysius over the nature of the meeting. They have a spirited argument over her claims, and Flynn threatens to have her dismissed. Sister Aloysius then reveals that she has spoken to one of the nuns at his former parish. Exasperated, Flynn reminds her that she has gone beyond Church procedures, but Sister Aloysius is determined to get the truth about his past. He pleads with her to no avail – he must leave St. Nicholas.

Scene five – the church 

Father Flynn celebrates a final Christmas mass with his congregants.

Scene six – the garden

Sister James has returned after a short absence while visiting a sick relative. She notes Father Flynn's departure, and Sister Aloysius reports he has been promoted to become the pastor of the St. Jerome Church and School. She admits her ruse – there was no phone call to the other nun – and her doubts and fears over her determined actions.