Thomas
Thomas holds Aloysius at gunpoint as Sister Mary takes a nap at the end of the play. This is a symbol of how she is training up legalism and not love to this young child, that he will eventually become her as he believes her way is the only way.
Stigmata
Diane reminds Sister Mary of a former student, Mary Jean, who the Sister claimed had a stigmata instead of her first period. This is a symbol of how human beings grant holiness and even saint-hood upon people through our opinions of them.
Cookies
Sister Mary Ignatius gives Thomas a cookie every time he answers a catechism question correctly. This is a symbol of training him to know the answers, but only because he is rewarded for knowing, not because he truly understands.
Shooting
Sister Mary Ignatius kills Gary after learning he has had a confession that morning of his sins. She says he will go to Heaven now. This is a symbol of her disbelief in God's love for all of us, so much so that she is unwilling to love him and believes killing him will save his soul rather than loving him.
3 Hours on the Cross
Sister Mary tells her students to stop complaining about their circumstances, as Christ withstood three hours on the cross with nails in his hands and feet. This is a symbol of her manipulation of these kids as she dismisses all of their issues as unworthy of any of her time.
