Mary only appeared for a short while in the film, because she was seen at the very end. She was first seen with her husband, Joseph riding on Small One (bought by Joseph from a boy earlier at night) while waving good-bye to the boy from a long distance and then, continuing their journey to the manger in Bethlehem where a bright star later shone; symbolizing the birth of their son, Jesus.
The "Hellfire" sequence of the film consists primarily of Frollo's prayer to blessed Mary ever Virgin. Roman Catholics do pray to blessed Mary to ask her to pray to God on their behalf, and because of her absolute purity, she is the perfect saint to ask regarding his inappropriate attraction to Esmeralda. However, in so doing Frollo reveals himself to be filled with sinful pride, lust, envy, and vengefulness.
Earlier in the movie, the Archdeacon sang "you can never run nor hide what you've done from the eyes, the very eyes of Notre Dame". This was the Archdeacon's way of saying that, from Heaven, blessed Mary bore witness to Frollo's murder of Quasimodo's parents, and thus Frollo needed to do something to avoid being damned by her. This is what convinced Frollo to adopt Quasimodo as his son.
- During the making of the "Ave Maria" segment of Fantasia, there were suggestions to have an image of the Virgin Mary appear in the last shot when it was intended to end with the monks (and possibly nuns) entering an actual church.