Act 1

Two police officers investigate the death of a local teen, Richie Lipschitz, and find the phrase "Nerdy Prudes Must Die" written in his blood. The story goes back in time, as the students of Hatchetfield High express their hatred of school. Steph Lauter, a popular student and the mayor's daughter, asks Peter Spankoffski, an unpopular nerd, to help her cheat on a test. One of their classmates, Grace Chasity, tells the teacher, and the two are sent to the principal's office ("High School Is Killing Me"). There, Pete impresses Steph with his sense of humor.

Later in the day, Pete and the other "nerdy" students lament about living their lives in fear of school jock Max Jägerman. Max attempts to flirt with Grace, who turns him down, and he vows he will have her ("Literal Monster").

Upon returning home from school, Steph's phone is confiscated by her father, Mayor Solomon, who says she can have it back if she improves her grades. She calls Pete and asks him to help her study. Pete's nerdy friends, Richie and Ruth, overhear the call and urge him to help her. As he goes to meet up with Steph, Pete wonders if he may actually be cool ("Cool As I Think I Am") only to be confronted by Max, who attacks him.

While Grace eats dinner with her family, she becomes flustered and inadvertently makes multiple sexual innuendos. She takes a bath to calm down, only to fantasise about Max. ("Dirty Girl"). Disgusted with herself, she decides Max "has to go".

The next day, Richie, Ruth, and Steph find Pete hiding in the bathroom with a black eye. Grace walks in on them and shares her plan to scare Max into never bullying anyone again ("Bully The Bully"). They lure Max to an old haunted house named The Waylon Place, which is said to have once belonged to a cult, under the pretenses that a party is taking place there. The group dons costumes and attempts to scare Max, but to their horror Max decides to overcome his fears by fighting the 'monsters' he sees. Steph reveals it was a prank, and Max is overjoyed, thinking the group planned the prank to help him overcome his fears. While thanking them, he accidentally falls through the house's floor. The other teens find Max mortally wounded, and Max, who thinks the group planned for him to get hurt, declares "nerdy prudes must die" before dying. Grace convinces the group to hide Max's body under the house's floorboards and tell no one ("Bury The Bully").

Two weeks later, everyone's lives have improved after Max's disappearance, and everyone is excited for the upcoming football game ("Go Go Nighthawks"). During the game, Richie, the team's mascot, hears Max's voice while alone in the locker room. Max's 'ghost' appears and kills him ("Nerdy Prudes Must Die").

Act 2

Grace's father, a realtor, reveals he has sold The Waylon Place. Scared Max's body will be found, Grace informs her accomplices, but are then all called to the principal's office. They are questioned by two police officers about Richie's death, which they did not know about, but is disclosed partway through the interrogation. Max's body is then found and the officers have to leave. A curfew is placed on the town, as the residents are encouraged to accuse each other of being the murderer by the Mayor ("Hatchet Town").

While doing lights for the school play, 'Barbeque Monologues', Ruth imagines what it would be like to be the star of the show ("Just For Once"). Max's 'ghost' appears again and kills her. Meanwhile, Grace attempts to throw the police off their trail by telling them that she saw a van with a bumper sticker from Hatchetfield's rival high school, Clivesdale, outside the Waylon Place on the night of Max's death. An officer asks if Grace left her bracelet in the principal's office after their last meeting. She confirms it is hers, and the officer reveals they actually found it in the Waylon Place. Grace steals a gun and flees before she can be arrested.

Pete and Steph meet up at a local coffee shop and argue about recent events, blaming each other while also accusing the other of being in love with them ("If I Loved You"). Grace finds them at the coffee shop and tells them that the police are onto them. When the police arrive, they accidentally target a local man (Paul from The Guy Who Didn't Like Musicals) allowing Grace, Pete, and Steph a chance to escape. Steph takes the gun away from Grace, and the three are found by Mayor Solomon.

Solomon takes the children to the Waylon Place and tells them to use the Black Book, a book containing dark spells, and use it to summon The Lords In Black, who will help them defeat Max. As the teens run off, Max kills Solomon. The teens discover the summoning ritual must be performed at one of many Black Altars in the town, one of which is at the school. On their way to the school, they are arrested by Detective Shapiro. The teens try to explain the situation to her, but she doesn't believe them until Max's 'ghost' appears ahead of them. The 'ghost' then appears in the police car and causes it to crash, but the teens are unharmed and escape.

Upon reaching the school, they perform the ritual in the gymnasium and summon The Lords In Black. The Lords agree to help in return for "the thing you cherish most," and one reminds Steph about the gun in her pocket ("The Summoning"). Max's 'ghost' appears in the gym, forcing the teens to flee.

Steph and Pete, now separated from Grace, realize that each one of them cherishes the other the most; one of them will have to die ("Cool As I Think I Am (Reprise)"). Pete tells Steph to shoot him, but when she does Max arrives just in time to catch the bullet. Before attacking Pete and Steph, Grace interrupts, offering to have sex with Max. He accepts, vowing to kill them later, and the two leave briefly. When they return, Grace reveals that she gave up what she cherishes most, her chastity, and The Lords in Black take Max away.

Weeks later, everything has returned to normal, and Pete and Steph attend homecoming together ("The Best Of You"). Grace attends with Jason, one of Max's former friends. Alone, the two share a kiss and Grace becomes disgusted. She reveals that she has the Black Book, and plans to use it to kill all "dirty dudes" ("Dirty Dudes Must Die").