The narrator of the first story in Dubliners, "The Sisters", is a nameless main character who is also a young boy, perhaps an acolyte. His best friend is an elderly priest of the Catholic Church who, at one point, took the narrator under his wing and would spend hours with him talking about religion, the faith, doctrine, and much more. This priest's funeral is taking place as the story develops.
The actual tale begins when Old Cotter, a family friend, visits the narrator's family (made of his aunt and uncle with whom he lives) and begins to talk about the recently deceased priest. His conversation hints at the possibility that the priest had an unhealthy relationship with the narrator, who is a child, and that no elder man should be dealing with younger fellows. This is a big deal because, as many of us know, James Joyce was extremely anti-Catholic and he used every opportunity he had to expose the double lives, abuse, and secrets of the Church in Ireland.
Back to the story..
When the narrator has this nightmare about the face of the priest, he sees the paralyzed face of Father Flynn trying to move his lips as if wanting to confess something. The narrator clearly has an inkling that Father Flynn might have died as a result of a dangerous double life, and this is the reason why his childish admiration for the priest slowly begins to change. He is not sorry that the priest is dead, he has a hard time feeling grief, and he admits to it. He also begins to detach from the story, as well as from his love for the priest. This is evident because the story ends with the tales of superstition that Father Flynn's two sisters used as an excuse to explain why their brother suddenly becomes insane, paralyzed, and dead.
On a darker note, it is believed that Joyce hinted at the possibility that Father Flynn diedof the tertiary stages of syphilis as a result of his sexual debauchery, and that the boy had been somewhat enthralled by this priest the way many abuse victims become lured to their abusers.