Act I
bare opens at a Mass on the Feast of the Epiphany in St Cecilia's Boarding School. Peter, an altar boy, is dozing off and having a nightmare in which he is outed and condemned by everyone ("Epiphany"). After Mass, Peter encounters Jason, St Cecilia's resident golden boy who is also his roommate and secret lover; Jason tries to assure Peter about their secret relationship ("You & I"). Peter asks Jason to audition for Romeo and Juliet, but Jason initially refuses. Alone, Peter reflects on his angst about his relationship with Jason ("Role of a Lifetime").
At "Auditions," drama teacher Sister Chantelle is dismayed by the lack of adept actors until Jason shows up, to everyone's shock. He and Matt, another altar boy, battle for the part of Romeo. In the end, Jason is cast as Romeo, Ivy (Peter and Jason's friend, whom Matt is in love with) as Juliet, Peter as Mercutio, Matt as Tybalt, and Nadia (Jason's overweight, sharp-tongued twin sister) as the Nurse. Jason attempts to console his sister, who wanted to play Juliet ("Plain Jane Fat Ass"). Opening a belated birthday gift, the siblings discover that Jason has been accepted into Notre Dame. The song was replaced with "Love, Dad" in the 2004 Off-Broadway production.
Later, Matt attempts to plan a small surprise birthday for Ivy. Lucas, the school's party boy, plans a trip to a rave, bringing along ecstasy and two other drugs (K and GHB) ("Wonderland"). Seeing a scantily-clad Ivy and its effect on Matt, Nadia decides to spend "A Quiet Night at Home" and play her cello instead.
At the rave, Peter dances with Jason and Ivy with Matt ("Rolling"). Peter tries to kiss Jason, who leads him outside. They argue over their secret relationship: Peter wants them to come out and make their relationship known but Jason refuses because he's afraid to be condemned and lose everything he has. Eventually, Peter and Jason kiss ("Best Kept Secret"); however, Matt has seen everything.
The next morning, the students gather for "Confession." Matt and Peter nearly spill their respective secrets to the priest, Matt about seeing the kiss and Peter about being gay. At rehearsals, Sister Chantelle realises she has her work cut out for her. Nadia jokes about Ivy's promiscuity, making the latter to consider the impression she has on the other students ("Portrait of a Girl").
Matt's little get-together becomes a huge party, thanks to Nadia's hand in the planning ("Birthday, Bitch!"). Peter accidentally eats pot brownies and begins flirting with Jason. A drunk Ivy does the same and Jason chooses her over Peter to save face, making Peter storm off. Matt also leaves when Ivy ignores his advances. Ivy asks Jason to kiss her as a birthday gift, and he reluctantly agrees ("One Kiss").
Matt leaves the party to sit alone with a bottle of wine, expressing his frustration while Peter is nearby doing the same. They then drink together and comfort each other ("Are You There?"). A drunk and high Peter then whispers to Matt the true nature of his relationship with Jason. Matt heads to bed and Peter has a vision of a Sister Chantelle-like Virgin Mary with angels, the Virgin telling him that he needs to come out to his mother ("911! Emergency!").
At rehearsals, Romeo and Tybalt's fight scene becomes real as Matt abandons the script and tackles Jason, calling him a faggot. They are separated by an angry Sister Chantelle ("Reputation Stain'd"). Peter tells Jason about his vision and asks him to come home with him for Spring Break so he can come out. Jason panics, afraid of what his father might do if he ever found out, and breaks up with Peter ("Ever After").
Later, Nadia sings a sardonic song she wrote about "Spring." Peter leaves for Spring Break without a word to Jason, and Ivy shows up at Jason's dormitory room to apologise for her actions on her birthday. Jason tells her it was cute, so Ivy goes in for more. Peter and Matt pine for each of their loves, Nadia wishes to be noticed, while Jason sleeps with Ivy, hoping it is the right thing to do ("One").
Act II
The second act opens in the school chapel which is decorated elaborately for Peter and Jason's wedding ("Wedding Bells"). The ceremony turns instead into Jason and Ivy's wedding, as this is really Peter's nightmare. Later, class ranks are posted, and Jason has achieved the valedictorian spot, once again besting Matt ("In the Hallway").
Ivy tells Jason that he is her first true love even though she has been with other boys before ("Touch My Soul"). Jason realises he is still in love with Peter and breaks off with Ivy, devastating her.
Peter calls his mother Claire, to come out but she evades the point ("See Me"). Claire hangs up, shaken and knowing what Peter wanted to say. Eventually her love for him is stronger than her religion and she introspectively accepts him ("Warning").
Two weeks before the show, Ivy misses rehearsals again, claiming to be sick. Sister Chantelle asks Ivy's inept understudy Diane to play Juliet. As Diane stumbles and forgets her lines, Peter takes over, and for a moment, all is well as Peter dances with Jason ("Pilgrim's Hands") until Ivy appears at the last minute. Sister Chantelle cancels rehearsals and Peter leaves. Ivy pulls Jason aside and tells him that she has something she needs to tell him and he agrees to talk before the student-led rehearsals. After the other students leave, Peter returns to pick up his things and Sister Chantelle tells Peter that she knows what is bothering him and that he is just as God wants him to be ("God Don't Make No Trash").
Nadia returns to her dormitory and argues with Ivy about missing rehearsals. She assumes it was because Jason broke up with her, but Ivy reveals that she is carrying his child ("All Grown Up"). Ivy finds Jason practising his valedictory address in the auditorium, and says that she is pregnant and she still loves him. Matt comes in and reveals to Ivy that the reason why Jason cannot love her is because he is still in love with Peter. At that point, Peter and Nadia arrive, and Peter, Jason and Matt exchange heated words. Peter admits he told Matt, and is not sorry for it. The rest of the cast, who were waiting for rehearsals to begin, heard everything as they were waiting in the auditorium ("Promise"). Everyone leaves, leaving Peter and Jason alone. Jason begs Peter for help; Peter says he tried and also leaves. Distraught, Jason reflects on his relationship with Peter, and how even through his fear he knows that it is the only thing that will comfort him ("Once Upon a Time"). Jason, having nowhere else to go, goes to the priest to ask if God still loves him and can forgive him. The priest ultimately says that Jason will only be fine if he denies his natural feelings ("Cross").
During rehearsal, Lucas passes out the drug orders and tells Jason that they're still cool. Jason tells Peter that he talked to the priest about their relationship to show Peter that he still cared ("Two Households"). Jason asks Peter to run away with him, but Peter refuses to run and thus tells him it's over, as he's had his fill of hiding and running away. Jason, thinking that means he's lost Peter for good, takes a lethal dose of GHB. As the school play begins, Jason again pulls Peter aside telling him that he has always loved him since they first met; Peter tells him he loves him too and if they part it's not goodbye. The lovers kiss ("Bare").
During the show, Jason becomes increasingly disoriented, and while delivering the "Queen Mab" speech, he loses his place and begins to hallucinate. During the masked ball scene, he collapses and reaches for Peter, who holds him as he dies ("A Glooming Peace"). Peter goes to Confession, intending to confront the priest about Jason's last visit. Peter accuses the priest of failing to show Jason empathy, and when the priest merely apologises for Peter's loss, Peter ironically forgives the priest ("Absolution").
At graduation, Peter, Matt, Ivy, and Nadia wonder whether or not they could have prevented Jason's death and consider the role they played in it. The graduates all move forward into a world that will yield more questions than answers ("No Voice").
