Aloysius
Sister Mary Ignatius hears that Aloysius is an alcoholic, beats his wife and keeps thinking about suicide. She tells him that these are venial sins, which to her means that he has turned out well. Her point of view is a metaphor for a fire and brimstone religious outlook that doesn't walk with people through the pains of life, nor the realities of their wrongdoing, but instead only looks at morality as a matter of absolutes: will it cause you to go to hell or not?
Thomas
Thomas answering all of Sister Mary's questions and doing everything she says throughout the play is a metaphor for how the Church has become a questionable institution. Apparently, the Church is seen as corrupting the youth rather than teaching and caring for them to grown into healthy adults.
Unanswered
Sister Mary repeatedly does not answer the question about why God allows evil on the earth. Her dismissal of the question is a metaphor for how the Church doesn't take the time to bring understanding to those who have real philosophical concerns. Instead, they ignore the question and make the divide even greater for themselves.
Retribution
Diane has come back to kill Sister Mary for how she had treated her, saying she made her into what she is. This part of the story is a metaphor for how those who influence us in our childhood categorically mold our future.
The Play
The former students put on a play for Sister Mary. It's a metaphor for how they were taught the stories of the Bible, but never were shown acts of love that would cause them to invest wholly in giving their lives to God. They learned to keep God at an arm's length, even with their knowledge of His story.
