It is the Feast of the Epiphany, and mass is being held at St. Cecilia's boarding school to welcome students back from Christmas break. Peter, an altar boy, falls asleep during the priest's homily and drifts into a nightmare in which he is outed by statues of saints, his mother, and his classmates (Epiphany). On his way to class after Mass, Peter finds his roommate and clandestine boyfriend, Jason, who tries to assuage Peter's frustration about their relationship (You and I). Peter asks Jason to audition for the Senior Play, a production of Romeo and Juliet, so they can spend more time together, but Jason refuses. The bell rings without Peter getting his desired kiss, and as he watches Jason walk away, Peter reflects on their relationship (Role of a Lifetime).
At auditions for Romeo and Juliet, Sister Chantelle, the school's no-nonsense drama teacher, is underwhelmed by the acting candidates – until Jason surprises Peter by showing up (Auditions). He and Matt, another altar boy, battle for the role. Sister Chantelle awards the role to Jason, and Ivy, the school's popular is his Juliet. Peter is Mercutio, Matt is Tybalt, and Jason's acerbic twin sister, Nadia, is the nurse.
Jason stays to console his sister, who wanted the role of Juliet (Plain Jane Fat Ass). She opens a letter she's received from their father, revealing that Jason has been accepted to Notre Dame, his first choice of schools.
At study hall, Matt tries to plan a small surprise party for Ivy's birthday while Lucas, St. Cecilia's resident party boy, tries to recruit everyone to go to a rave (Wonderland). In his best white boy rap, he introduces the students to two drugs: K and GHB.
The night of the rave, Nadia decides not to go, after seeing the skimpy attire on Ivy and the attention it's generating from Matt. When everyone leaves without her, she takes out her cello and spends another quiet night by herself (A Quiet Night at Home).
At the rave, Peter dances closer to Jason while Ivy dances closer to Matt (Rolling). As Peter goes in for a public kiss, Jason pulls him outside. They argue over the nature of their relationship, Peter wanting to be more open, Jason telling him that the rave is different from school (Best Kept Secret). Peter finally gets his kiss; it's not public, but it is, unbeknownst to them, witnessed by Matt.
The following morning, the groggy students gather for their least favorite St. Cecilia's activity: confession (Confessions). Peter comes close to telling the priest how he feels, and Matt comes even closes to telling him what he saw. At first rehearsal that afternoon, Sister Chantelle realizes she has her work cut out for her. During a break, Nadia makes a crack at Ivy's promiscuity, and Ivy reflects on the image the students have of her (Portrait of a Girl).
The intimate party Matt was planning to impress Ivy gets commandeered by Nadia, who turns it into a full-scale bash (Birthday Bitch!). Peter stuffs his face with brownies, not realizing they're pot brownies, and begins flirting openly with Jason. Ivy, drunk, also flirts openly with Jason, and when he chooses Ivy over Peter to protect his image, Peter storms off. Ivy dismisses Matt's advances, concentrating her energy on landing Jason. She asks him for a kiss for her birthday, and he reluctantly agrees (One Kiss).
Both Matt and Peter retreat to the solace of the church's chapel, where they ask God for answers (Are You There?). There, Matt takes the opportunity to ask about the "nature" of his relationship with Jason. Peter, still high from the brownies, confesses all to Matt, desperate to talk about his confusion. When Matt abruptly leaves, Peter realizes what he has done, but is stopped when he has a second "vision" in the church: Mother Mary appears in the guise of Sister Chantelle. She and her two angel sidekicks tell Peter it's time to tell his mother his secret (911! Emergency).
At rehearsal the following day, Jason and Matt's fight scene turns real, and they have to be separated (Reputation Stain'd). Peter tells Jason about the vision he had, and that he wants Jason to go home with him over Spring Break so he can tell his mother about them. Jason's had enough, and breaks up with Peter (Ever After).
As students pack to go home for Spring Break, Nadia sings a self-penned ode to spring (Spring). Peter leaves wordlessly with his mother, as Ivy shows up at Jason's dorm to apologize for throwing herself at him at her party. When Jason gives Ivy the impression that he enjoyed kissing her, Ivy goes in for more, and Jason gives in. As Peter misses Jason, Matt pines for Ivy, and Nadia begs to be noticed, Jason has sex with Ivy in his dorm room, hoping that this is the right thing to do (One).
Act Two opens in the church, where the scene is set for an elaborate gay wedding. Peter is dreaming again, this time about a civil ceremony with Jason (Wedding Bells). After Mass, class ranks are posted; Jason has once again bested Matt, walking away with the valedictorian spot.
Ivy wonders why Jason hasn't called her since that night, telling him that she has, for the first time, fallen in love (Touch My Soul). Jason, realizing that the feelings Ivy is describing are exactly what he feels for Peter, breaks things off, devastating her.
Peter phones his mother to finally tell her his secret. But she won't let him say the words, continually changing the subject (See Me). She hangs up on him, but she knows what he wanted to tell her. Alone, she wonders how to deal with what to her is a confusing and earth-shattering revelation (Warning).
With two weeks to go before the show, Ivy misses yet another rehearsal, claiming illness. Sister Chantelle asks the understudy to read with Jason, but she can't remember her lines. Peter steps in, and for a moment, all is perfect, as he dances with Jason (Pilgrim's Hands). Ivy finally shows up, breaking the spell. Sister Chantelle cancels rehearsal, and tells the students they are on their own for rehearsal – she's through. Ivy begs Jason to talk to her, and he agrees to meet her before the student-led rehearsal that evening. As students move to exit, Sister Chantelle tells Peter to stay. She knows what's bothering him – and tells him that he's exactly as God intended him to be (God Don't Make No Trash).
When Nadia returns to the dorm room, she confronts Ivy about missing rehearsal, assuming she's moping about her brother breaking up with her. They argue, and Ivy reveals the true reason she's been missing rehearsal: she's pregnant (All Grown Up).
Ivy leaves and finds Jason practicing his valedictory address in the auditorium, and there she tells him her news. As Jason reels from the revelation, he wonders whether this is exactly what he wanted all along? He tells her that maybe he does, in fact, love her, but at that moment, Matt steps out of the wings and reveals Jason and Peter's relationship. Peter shows up, then Nadia – and then the entire cast is revealed, having heard everything (Promise).
Jason returns to his dorm room and watches Peter sleeping peacefully (Once Upon a Time).With nowhere to turn, Jason goes to the priest to ask the question that has tormented him for years – does God still love him? When Jason presses the priest for an answer, the priest ultimately condemns him (Cross).
As the students lead vocal warm-ups for the show, Lucas passes out their afterparty drug orders (Two Households). As the show is about to begin, Jason pulls Peter aside and makes a plea: run away with him. Peter tells Jason he's done running. Jason nods, knowing it's finished; just before going on, Jason takes a lethal dose of GHB. Right as everyone moves into places, Jason pulls Peter aside to tell him he loves him; the share a final kiss (Bare), and the play begins.
As the play unfolds, Jason becomes increasingly disoriented. During the Queen Mab speech, he loses his place completely and begins to hallucinate (Queen Mab); this segues into the masked ball scene, where Jason has increasing difficulty keeping time as the players switch partners, and he collapses, reaching for Peter (A Glooming Peace).
Peter visits the confessional, confronting the priest about his final visit with Jason. Struggling to come to terms with his role in Jason's death, he asks Peter for forgiveness, which Peter grants (Absolution).
At graduation, Peter, Matt, Ivy and Nadia try to process their grief over Jason's death, trying to understand it and wondering whether they could have prevented it. As the senior class of St. Cecilia's graduates, the chorus of students crescendos and they move forward into a world that offers more questions than answers (No Voice).