I would suggest that a critical motif in Shanley's play is the absence of certainty. Shanley is able to construct the title as a motif because of its reappearance throughout the drama. The sermon that Father Flynn delivers at the drama's exposition is about uncertainty and doubt as a potentially unifying force. The closing words that Sister Aloysius speaks are, "I have doubts! I have such doubts!" Sandwiched in between both verbal expressions of doubt is a mass of confusion and lack of certainty. Shanley is able to take a metaphysical idea and create a motif from it. Nearly every one of the characters experiences doubt as a state of being in the world. This aspect of characterization is so dominant that it becomes a motif in the drama.
The play speaks to the result of lives that previously believed in certainty, only to be shrouded in doubt and the lack of absolutism. For example, Father Flynn evokes doubt from nearly everyone with whom he interacts. At the same time, it is never clear what Father Flynn exactly is. The doubt created becomes a motif because every moment he is seen, the viewer is not entirely clear if he is a child molester or if he is a good man besieged by the most unspeakable of conditions. Like Sister Aloysius, the viewer is nothing more than the sum total of "such doubts." Sister James walks with the motif of doubt within her being. She is a young teacher trapped between the formalism of Sister Aloysius and the student- centered aspect that she craves. She comes to question everything about her professional and personal consciousness. When Sister James admits that Sister Aloysius has "taken away my joy of teaching. And I loved teaching more than anything," one sees a woman in doubt. Doubt has crept into every fiber of her being and, as a result, her very presence on stage is a motif of doubt, testament to the destructive nature of uncertainty. Mrs. Muller embodies the same position of doubt and uncertainty. As a character, her presence in the world is formed by doubt. She has doubt about the sexual identity of her son, the capacity for nurturing that her husband displays towards Donald, and presents doubt regarding the entire encounter between Father Flynn and her son. Doubt as a motif is present with Mrs. Mueller more than anyone else because it haunts her, lingering around her. Nearly every word she utters is a confirmation of doubts that are present. The lack of certainty is so much a motif that it even extends to a judgment of Mrs. Muller. She might be overwhelmed, or focused on the potential future for her child, or seeking to merely protect him from the horrors of an abusive father. In the end, she is doubt personified and confirms that the motif of doubt is evident in both her actions and her entire presence. Sister Aloysius demonstrates how doubt is a motif in the play. It has never entered her being. She carries herself with nothing but certainty and absolutism. She pursues Father Flynn with vigor and intensity. She runs her school with strict order and discipline. If there was one character that resisted doubt, it would be Sister Aloysius. Yet, when we see that she crumbles under the weight of doubt at the end of the drama. Her capitulation demonstrate doubt as a motif, waiting for the Sister. In this, the motif of doubt is evident in how it impacts each character.