Religion
Religion is at the forefront in this play as the Sister takes into her hands what is right and wrong, and leaves no room for a conversation to be had regarding her authority and knowledge of what is sinful or not. We learn that knowledge of God without relationship with him creates a woman who's heart has been covered in stone and her character looks nothing like Jesus.
Sin
Sin is at the forefront of the second half of the play as the Sister's former students enter with a great deal of it. Sister Mary Ignatius is quick to be judge and jury and soon become executioner, taking Gary's life in order to send him to heaven before he sins again by sleeping with another man; and she kills Diane in self defense, stating she doesn't even have to confess this sin as she was defending her life. The good Sister has created a system of loopholes to serve her belief system, but failed to truly connect with these kids in a way that was beyond head knowledge and discipline.
Relationship
Relationship, or the lack thereof is a major theme of this play. We witness former students returning to their teacher who has wounded them deeply as children, and these wounds carry forth to the present time in their adult live. Sister Mary was teaching them to obey her, and by so doing created a false notion of what obeying God must be like as the kids began to believe that to obey God was like obeying the Sister and the Catholic Church. It is Sister Mary Ignatius' lack of relationship with God that has poured out upon her students as all they see is religion, not love.