A continent of certainty in a sea of doubt, Sister Aloysius reveals her implacable nature in a contest of wills with Father Flynn (Brían F. O'Byrne) when she's tipped to a student's odd behavior by a nervous younger nun, Sister James (Heather Goldenhersh). Meaning no harm, Sister James mentions that a student named Donald Muller, the only African-American at the St. Elizabeth Ann Seton-founded school, had recently returned to class with alcohol on his breath and looking upset after a talk with Father Flynn. Sister Aloysius concludes, on the basis of faith in her own instincts, that Father Flynn has seduced the boy. She sets out to extract an admission from the astonished priest and refuses to accept the explanation that he'd held the secluded chat because he'd caught the Muller boy drinking altar wine and wanted to keep the incident quiet, since the consequence of such a transgression would be the boy's removal from his altar boy position. Father Flynn contends that such ejection would lead to Muller's being ostracized more than he already is.
Although Sister James accepts the situation as described, Sister Aloysius doesn't. She becomes further convinced that Father Flynn is a pedophile when she summons the boy's mother (Adriane Lenox), to her spare office and learns that the lad is homosexual. (Because of this proclivity, he's regularly beaten by his father.) Relentlessly confronting Father Flynn -- whom the audience sees forthrightly sermonizing on uncertainty as well as gruffly coaching the school's basketball team -- Sister Aloysius won't accept his repeated insistence that he's innocent of untoward action.
The chilling beauty of the play originates with the specific example that Shanley employs to moot one of organized religion's most recurring issues: the place that doubt has in the minds and hearts of the faithful. Refusing to supply a pat answer to the ever-present quandary, Shanley is cunning as he pits a self-proclaimed religious woman who brooks no reservations about her beliefs against a clear-cut religious man who does. The playwright doesn't confine the argument to the philosophical wrestling match on stage; before the intermissionless 90-minute play ends, he's provided information on Sister Aloysius and Father Flynn that leaves patrons grappling with their own doubts.