The play begins with one of those adversaries, Bobby, whispering slurs to fluster Pharus as he sings the school’s prayerful anthem, “Trust and Obey.” Bobby (J. Quinton Johnson) is an obvious hothead homophobe, complete with mama issues, but he is also the nephew of Headmaster Marrow (Chuck Cooper) — so it’s Pharus who gets in trouble. Even so, Pharus refuses to rat Bobby out, in misguided deference to the school’s code of honor.

This is the first of many plot points that feel both obvious and false, like pieces of the wrong puzzle ham-hammered into place. Too frequently, information that if delivered sooner would have forestalled the plot completely is delivered hastily later, as if to sweep it under a dorm bed. In any case, Trip Cullman’s tonally blurry staging for the Manhattan Theater Club does not help you understand what to make of such logical inconsistencies, though it is at least swift enough to keep you from dwelling on them.

But a similar problem eats away at the credibility of most of the characters as written. Two of the choir boys, Junior (Nicholas L. Ashe of “Queen Sugar”) and David (Caleb Eberhardt), get approximately one trait each. Junior is pleasantly dim; David is tortured by something you’ll see coming a mile away.

The adults have it worse. Even the venerable Mr. Cooper can’t make Marrow coherent in his fecklessness, and a subplot in which a retired teacher returns to the school to lead a seminar in “thinking” has the subtlety of a shoehorn. It’s not just that the teacher, played charmingly by Austin Pendleton, is a caricature of a fuddy-duddy. (As part of an assignment, he suggests that the students “get i-mail or g-tunes.”) It’s that he is used like a piece of furniture, with no story of his own, for others to walk around or trip over.

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It likewise becomes difficult to sort out how much of the action results from ambient gay animus toward Pharus and how much from his own lordliness: He’s the best singer, and he knows it. (His name means “lighthouse.”) With good cause, Marrow calls him gifted, ambitious and “operating.”