A young boy reflects on the impending death of his friend Father Flynn. Knowing that after three strokes the paralyzed priest has little time left, the boy makes a habit of walking past Father Flynn’s house, looking for the light of the traditional two candles placed on a coffin that would indicate his death. Each time, the boy thinks of the word paralysis. One night at his aunt and uncle’s house, the boy arrives at supper to find his uncle and Old Cotter, a family friend, sitting before the fire. Old Cotter has come to the house to share the news that Father Flynn is dead. Knowing that everyone waits for his reaction, the boy remains quiet.

While the aunt shuffles food to and from the table, a conversation ensues between the uncle and Old Cotter, and the uncle notes the high hopes Father Flynn had for the boy. He hints that Father Flynn planned to prepare the boy for the priesthood and remarks on the friendship between them. Old Cotter, however, thinks of Father Flynn as a “peculiar case” and insists that young boys should play with people their own age. While the uncle agrees with Old Cotter, the aunt is disturbed that anyone could think critically of Father Flynn. She asks Old Cotter to clarify his point, but Old Cotter trails off and the conversation ends. That night, Old Cotter’s comments keep the boy awake, and he dreams of Father Flynn smiling and confessing something to him.

The next morning the boy visits Father Flynn’s house, where a bouquet of flowers and a card hang from the door handle. Instead of knocking, he walks away and reminisces about the time he spent there. He used to bring Father Flynn snuffing tobacco from his aunt, and Father Flynn would teach him things, such as Latin pronunciation and the parts of the Mass. Remembering Old Cotter’s cryptic comments, the boy then tries to recall more of his dream from the night before, but he can remember only a Persian setting—he cannot remember the end. That evening the boy visits the house with his aunt, and they kneel at Father Flynn’s open coffin with one of Father Flynn’s sisters, Nannie, to pray. Afterward, the three retire to another room to join Eliza, Father Flynn’s other sister. Over sherry and crackers they discuss Father Flynn’s death, his taxing career as a priest, and the helpful services of Father O’Rourke, another priest who anointed Father Flynn and completed all of the necessary paperwork and death notices. All the while the boy remains quiet. The story ends with Eliza’s recollection of Father Flynn’s increasingly odd behavior, which started with dropping a chalice during Mass. When one night Father O’Rourke and another priest found Father Flynn shut in a confessional box, laughing to himself, they finally realized he was sick.