NEW YORK, NY.- Here are a few things Sister Aloysius cannot abide: ballpoint pens, “Frosty the Snowman,” long fingernails like Father Flynn’s, Father Flynn himself.

She is what you’d call a forbidding nun, a Sister of Charity without much of it. (Her name means something like “warrior.”) The principal of a Catholic school in the Bronx in 1964, she defines a good teacher as one who is a discomfort to her students, a “fierce moral guardian,” not a friend.

“If you are vigilant,” she tells young Sister James, “they will not need to be.”

But Father Flynn, following the spirit of the recent Second Vatican Council, and presumably his own inclinations, does not lead with fear. In ministering to his mostly Italian and Irish congregation, he seeks to give the church “a more familiar face.” His sermons are warm, told with jokes and accents. He coaches the boys’ basketball team. Add to Sister Aloysius’ catalog of unholy tendencies his suggestion that they occasionally take the students for ice cream.

Even if nothing else set these two forces in opposition, there would be enough here for a fine play about varieties of faith. But John Patrick Shanley’s “Doubt: A Parable,” first seen on Broadway in 2005, is much more than that. It is a sturdy melodrama, an infallible crowd-pleaser, a detective yarn, a character study and an inquest into the unknowable.

It is also, in the handsome revival that opened Thursday at the Todd Haimes Theater, something I hadn’t really noticed before: a battle of the sexes. For in the church of that day, as perhaps in our own, mutual distrust often arose between the men who had all the power and the women who saw how they used it.

Why, after all, should Aloysius (Amy Ryan) already dislike the popular Flynn (Liev Schreiber) when the action begins? Why should she suspect that behind his “more familiar face” lies overfamiliarity? Is it his ballpoint pen? Those detestable fingernails?

On little evidence, she soon lets her uneasiness fix on Donald Muller, the school’s first Black student. A lonely eighth grader, isolated by his race and other things, too, he is, she intuits, easy pickings for a pedophile. When Sister James (Zoe Kazan, wonderfully mousy) reports that the boy has alcohol on his breath after a visit with Flynn in the rectory, Aloysius goes into prosecutorial mode. Flynn says Donald was found drinking altar wine in the sacristy, but Aloysius is sure Flynn gave it to him.

“The little sheep lagging behind is the one the wolf goes for,” she explains to the scandalized Sister James.

In the wake of the church’s pedophilia scandals, which were becoming big news when the play premiered, it takes immensely skillful writing to cause an audience to suspend its judgment in the face of such a charge. More so to leave people rooting, as many will, for the vindication of the accused.

Yet Shanley, having attended church schools in the Bronx, has calibrated the play’s arguments, and the timing of its revelations, like a fine watch he’s studied for years. To temper the impression of Aloysius as a righteous crusader, the play makes her an insufferable gargoyle. (This also makes her hilarious.) To temper Flynn’s good humor and heartiness, the play makes him handsy. (At one point, he pats Sister James in sympathy, despite the don’t-touch-a-nun rule.) Each statement from one is answered by a diametrically opposed statement from the other.

“Innocence can only be wisdom in a world without evil,” Aloysius warns Sister James, taking pride — that cardinal sin — in her flintiness.

“It’s an old tactic of cruel people to kill kindness in the name of virtue,” Flynn complains to her later.

Both precepts seem plausible, even if one is harsh and one loving, and both are chewily written. The entire play is like that: ideally worded, ingeniously structured, sinewy and swift. It never lets you, or poor Sister James, reach a conclusion as to which, if either, of her superiors is right. By the time Shanley takes the astonishing step of having Aloysius interrogate Donald’s mother — Quincy Tyler Bernstine, scoring big in a short but vividly counterintuitive role — you no longer know what you believe.

Still, if you’re like me, you may lean more heavily to one side than the other. In this regard, Scott Ellis’ production for the Roundabout Theater Company has not yet reached the ideal balance; Ryan, stepping in for an ailing Tyne Daly, has had just a few weeks to prepare. Her take on Aloysius is smart and uncompromising but a bit small in crucial moments, leaving the splendid Schreiber — a strapping 6-foot-3, with a tough guy’s brush cut and a thick Bronx honk — to outman her. (Brian F. O’Byrne, who played Flynn in 2005, was scragglier, and Cherry Jones, as Aloysius, more imposing.) Schreiber is also about the same age as Ryan, not a couple of decades younger, as written.

The climactic scene between the nun and the priest, as their certainties finally collide, is thus slightly muffled in this production, which doesn’t take enough time to let the momentousness of what’s happening sink in. In truth, that’s also a glitch in the play’s joinery: Something has fundamentally shifted, but Shanley refuses to say what it is. (A crucial coda is still to come.) I think this glitch is why some critics have found “Doubt” a bit slick: Like procedurals, it withholds information to maintain suspense, but unlike them it does so permanently. It’s manipulative.

Is that really a criticism, though? I want plays to manipulate me, and it is often truly the case that we cannot know the truth. For a man like Flynn, who has “things he can’t say” in 1964, it may well be that he is innocent of Aloysius’ charge but guilty of something else.

Such ambiguity, necessary and humbling, is an enduring concern for Shanley, who is the subject this winter of an accidental New York retrospective. The same unsettled judgment lies at the heart of his more directly autobiographical “Prodigal Son,” in which another troubled boy — played, in its 2016 Manhattan Theater Club premiere, by Timothée Chalamet — comes under the sway of another Catholic mentor. Underage drinking is again involved, and also sexual impropriety.

Still, Shanley does not quite condemn the teacher in “Prodigal Son,” modeled after a central figure in his own youth, except in using his real name; moral inquiry, the play demonstrates, is not the same as moral certainty.

Nor is it the same as moral inconsequence; some people do pay for their sins.

As I see it — your takeaway may vary — “Doubt,” in this production, throws Aloysius under the bus for her pride. That seems realistic. The Father Flynns of this world often bounce back from much graver accusations, not because they are necessarily innocent but because, with a collar or not, they are men.

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‘Doubt’

Through April 21 at the Todd Haimes Theater, Manhattan; roundabouttheatre.org. Running time: 1 hour 30 minutes.

This article originally appeared in The New York Times.