From the numerous flashbacks and memories scattered through the story, Father Flynn is shown to have been an intellectual priest, trained in Rome and having a strong religious vocation, but unable to cope with the mundane daily routine of being a parish priest - which finally led to his collapse. The boy narrator is seen to have initially admired Father Flynn and looked up to him, and later felt deeply sorry for him and guilty about not having visited him in his last days - all of which the narrator must conceal from his adult environment, where Father Flynn is considered to have been a complete failure, his death is in fact regarded with relief and he is considered to have been a bad example from which the boy must be preserved.
The choice of the title is quite curious as the story clearly focuses on the boy's relationship with the dead priest and the sisters Eliza and Nannie seem to be quite marginal to it. Joyce's intention in giving this title to the story is far from obvious, though a common theory is that the title comes from the fact that the priest's sisters are shown to be the only ones (besides the boy) who really knew and understood what Father Flynn was going through in the monotonous life of a priest in Dublin.