Experiencing John Patrick Shanley’s play, film or opera for the first time, the unwary spectator might be initially convinced of Father Flynn’s culpability for committing unspeakable crimes. In the wake of the scandal that has rocked the Catholic Church over the past two decades, the accused priest is generally considered guilty unless proven otherwise. But the main purpose of the narrative is not to investigate any failings of the 2,000-year-old institution, but use it as a backdrop to explore a more fundamental notion – that of certainty.

The work is outlined by a pointed dichotomy. Flynn is presented as a Vatican II-style priest, progressive, self-indulgent, at times imperious, yet vaguely effeminate, sporting uncommonly long fingernails. He is popular with his parishioners, coaches basketball, enjoys secular songs and the sound of his own voice. Juxtaposed in direct opposition is Sister Aloysius, a stern, terse widow, a woman knowledgeable in the ways of the world, a nun feared by all (though likeable and humorous at rare moments), who personifies all clichéd impressions of a fierce ruler-wielding schoolmistress. Her no-nonsense approach dismisses all types of pleasure and convenience, from Christmas tunes and ballpoint pens to sugar and costume jewelry. She is not above lying to achieve her purposes, and she is not without her flaws, as we discover by the end of the drama.

A closer examination of the text reveals how these two polar opposites explore the parameters of “doubt.” Set in a crumbling rough-and-tumble Bronx neighborhood in 1964, the story is framed by the turmoil of the Civil Rights Movement, Church reform and the threat of global conflict. The quiet protagonist, Donald Miller, is St. Nicholas School’s first African-American student, a gesture reflecting an early attempt at the desegregation of public and private educational institutions. The First Vatican Council, a consolidation and affirmation of the pope’s power in response to Rome’s occupation by Italian Risorgimento revolutionaries in 1870, was overturned by the Second Council, opening up the Church to lay people. One no longer had to merely “pay, pray and obey” – it was the end of ecclesiastical apartness, the clergy now being close family friends and members of the community, delivering mass in English to the occasional accompaniment of a guitar. Meanwhile, military conflict loomed in the wake of the Cuban Missile Crisis and developments in Southeast Asia.

In the light of these momentous events, the opera opens with a sermon on the theme of hopelessness, using as a preamble to a parable the recent murder of President John F. Kennedy, an event that shocked and deeply moved the entire nation. Flynn sees doubt as a unifying, communal emotion, whereas outside the scope of the drama (subtitled “A Parable”), it becomes destructive and contentious as Flynn’s reputation is itself assassinated. During this scene, the priest privately reveals he has indeed done something wrong, although we never truly learn what that is. In an opening soliloquy, Sister Aloysius discloses her own reservations about her suspicions, echoed again in the opera’s final lines.

The two scenes that follow establish Sister Aloysius as a fierce disciplinarian, both to her students and her fellow sisters. She plants mistrust into the thoughts of the nuns in her charge, particularly those of Sister James, whose innocence will ultimately be obliterated. James’ naïveté is tested as Sister Aloysius berates her for lax classroom discipline and reminds her of the male-dominated Church in which the two nuns are ultimately powerless. It is also the first time both sisters see Father Flynn with his arm around Donald Miller through a window (the opening and shutting of windows being a common theme). From past experience, Aloysius begins to suspect the worst.

Physicality is another of Father Flynn’s traits; thus he may be perceived as unusually familiar with the male students. The recoil of one, William London, becomes the primary (and rather thin) evidence against the priest (by way of disgust and “knowing looks,” the film suggests the theory that London might have also received unwanted attention). Flynn is shown at ease with the boys he coaches, at once their friend and confidant, further accented by his later “bull session” over cookies and milk. There is some irony in his dating advice, given that he has probably been cloistered in the seminary since his teen years, with no authentic life lessons upon which to draw (the very thought ridiculed by Sister Aloysius, who as a once-courted married woman, has once lived on the outside).

Greater complexities develop in the following sequence of events. During a dreamy montage, a jocular dinner for the priests is contrasted with the austerity of the same for the sisters, while an intoxicated Donald is caught by Mr. McGuinn (who never actually sees him drinking the altar wine). Next, Flynn stealthily stows a t-shirt in a locker, a peculiar action quietly observed by Sister James. Clearly, she has concerns of her own, which she confides in the elder sister as she has been instructed to do. Refusing to follow Church procedures and cross the garden (the gulf that separates the priests from the nuns) to report to the monsignor, Aloysius takes matters into her own hands. Using Sister James as her pawn, she rather deviously strategizes to trick Flynn into revealing his secrets.

Of course Flynn is piqued by the insinuations and prepares to leave, but when the use of alcohol is mentioned (historically, a common enticement in cases of minor assault), he turns to minimize the situation. He has a ready answer (premeditation also plays a part) blaming the incident on Donald and his own actions as a cover-up of the offense. From the moment he takes Aloysius’ seat of power, the priest reveals a certain degree of conceit, a sense of being beyond the law with a quick-and-ready answer for every question (a further symptom of an abuser). Or is he just accurately reporting what happened?

At the top of Act II, Father Flynn gets his revenge, arrogantly preaching on the consequences of gossip by way of another parable. Confident he has the situation well under control, he openly mocks the nun. The scene that follows is an even wilier moment as Flynn skillfully “seduces” Sister James over to his side in the garden, a place where priests and nuns are not to be discovered in pairs. With his usual smooth patter, effortlessly spoken both at the altar and in daily life, Flynn adroitly explains away the t-shirt (though why Donald would be embarrassed by its personal return is a little unclear). The presence of a cawing crow (never a harbinger of anything pleasant) is significant if slightly ambiguous. Is it symbolic of the black-attired and grim Sister Aloysius making false accusations or of a dark, guilty conscience? The ever-physical Flynn goes as far as to put his arm around Sister James in a sympathetic gesture, another violation of Church decorum. With his speech about love, compassion and humanity, is he actually finding a kindred spirit in the young nun, also a pure soul trying to do good works? Or is he manipulating her gentle nature to rationalize his own abhorrent behavior? It is an additional question mark giving us pause.

The meeting with Donald’s mother is a decisive moment in the drama. Unlike the other principal players, Mrs. Miller lives in the real world, where she has to be coolly pragmatic. During her conversation with Sister Aloysius, she emphasizes the lack of any real evidence the nun has to support her claim. Rather than being horrified by the possibility that her son is being mistreated, she soberly deals with issues before her. Donald must remain at St. Nicholas School, as he was beaten at public school for being “different.” (For a 1960s-era individual, Mrs. Miller is surprisingly supportive of her son’s homosexual tendencies). His father hates him for the same reason, so Flynn maintains a surrogate role, and she is grateful for that attention. She fears her son may be ostracized if any rumors were made public, race being a very real factor in her mostly Caucasian external world. Where Sister Aloysius’ black and white microcosm sees things in either light or darkness, Mrs. Miller (clearly the most insightful of the four leading characters) sees the world in tones of gray.

The original drama’s penultimate scene is the final showdown between priest and nun. Flynn’s transformation from self-assured and vindictive to a destroyed man could be a telling sign pointing to his guilt and is presented in stages. First he proclaims that Sister James believes him. Next he discloses the fact that Donald’s father beats his son. None of this working, he threatens to have Aloysius removed from her position. Unnerved by the revelation that St. Nicholas is the priest’s third parish in five years and that Aloysius has been digging into his past by calling his previous appointment, Flynn is thunderstruck by what is happening to him and desperately appeals to the nun’s compassion (where he will find none). It is clear he has done something wrong (having once admitted it to his confessor), and Sister Aloysius tries her very best to beat an admission out of him in an entire reversal of power. Yet, she never succeeds, implying a certain innocence of those specific allegations.

“His resignation was his confession,” so Sister Aloysius reasons in the final scene, even though in telling a falsehood (the call to Flynn’s previous parish never took place) she has committed a mortal sin. Now that she has achieved her goal – Flynn’s removal – and has had some time for reflection, the sister’s moral fortitude crumbles in an emotional cascade of doubts. With the caw of the crow, her tragic flaw, that righteous, iron-clad conviction has flown away, dissipating in a flood of uncontrolled uncertainty. With regard to faith, “doubt” may be an evil but is far from being a weakness – it can reveal the consequences of narrow thinking and a greater understanding of the human experience. The truth is rarely simple.