Dial M for … What?

We’re cool with murder, in our way. The gravest of horrors in real life, it’s a given in our entertainment — that precipitating act required so that our CSI characters can start sniffing through their interchangeable adventures. In countless light mysteries, ones starring Angela Lansbury or — bizarrely — Jane Austen, it’s the one aberration that must be dealt with to set a grand world right again. Homicide: It gives our heroes something to do.

Detective stories depend upon our willingness to treat murder as an abstraction. Sometimes, though, a writer challenges the genre — and us — with crimes we can’t wish away as morbid exceptions. In Michael Chabon and Robert Harris, familiar clues and skullduggery lead detectives to the Holocaust. And right now, at the Kansas City Repertory Theatre, Bronx nun Sister Aloysius snoops around a case of priestly molestation. Who’d dial M for that?

That’s Doubt, the agreeable yet gently queasy mystery-drama that won author John Patrick Shanley a Tony, a Pulitzer Prize and rights money from half of the community theaters in the country. Shanley blends things meant to be left apart. Here, he combines his Sister Aloysius, a patently unbelievable meddler right out of a book-club paperback, with a scandal that is this country’s most cut-and-dried crisis of faith in generations.

He even dares to write early scenes in the mode of quaint church comedies such as Going My Way. Sister Aloysius, the principal of St. Nicholas’ Academy in 1964, bemoans such indulgences as pop songs or ballpoint pens. She scolds Sister James (Gardner Reed), a naïve young teacher, for taking pleasure in teaching history, and we hear occasional complaints about her severity. She’s played, though, with radiant humor by Laurie Kennedy. Her lips purse genially, her smile spreads warmly, and her closed-mindedness comes across more as comic fussiness than law. She’s the kind of secretly humanistic church authority that liberal authors fantasize about.

Were it not for the “mystery” she’s soon saddled with, Sister Aloysius, we suspect, would be nudged into modernity by Sister James. And set-designer David Potts’ gorgeous gray-stone church would grow alive with fresh color.

Instead, Sisters James and Aloysius come to suspect Father Flynn (Eric Thal), their parish priest, of inappropriate congress with the church’s only black altar boy. As the material grows more uncomfortable, Shanley is slow to let up on the old-Hollywood-style comedy. Much of Sister Aloysius’ first confrontation with Father Flynn is played for the kind of laughs you might expect from one of those dinner theaters that tasks you with solving a murder. Shanley (and director Stephen Rothman) make much bustling business over who is sitting where in the room. Because it’s well staged and we’re familiar with scenes like this, we laugh a little, despite the situation’s gravity — and despite strained performances from Reed and Thal.

With all these different genres getting it on, the audience is sometimes confounded. A heartbreaking later scene between Sister Aloysius and the mother of the boy who may have been abused builds to a pitch that drew curious crowd reactions. The mother (a marvelous Gina Daniels) knows nothing of Sister Aloysius’ suspicions. After ascertaining that her son is not in traditional “trouble” and that he is likely to graduate on time, she says, with relief, “That’s all I care about. Anything else is all right with me.”

As Sister Aloysius cocked an eye up, ready with the bad news, a third of the audience laughed. Of course they did: They’d been trained to. We’ve seen this same kind of “here comes the bad news” gag thousands of times in farces and sitcoms, and we know our role in such a scene.

But that laughter is uncomfortable, thankfully, and it soon fades. This is Shanley’s real achievement: Doubt tells us little about pedophilia but much about genre. Why are we so easily tricked into enjoying the unspeakable?

By the end, Sister Aloysius is in a full-on noir. Despite the fact that, as played by Thal, the angry Flynn comes to sound a bit like a professional wrestler haranguing an opponent, the final scene is urgent entertainment, frustrating in the right ways: no clear answers, no easy conclusions. Crime, here, is not a puzzle to be solved — it’s deep and pervasive, a stain that no amount of wiping can wash away.