Zombie Prom opens at Enrico Fermi High School. The students go through their daily routine and the audience meets Jonny, a rebel who spells his name without the traditional 'H.' We also meet Miss Strict, the principal of Enrico Fermi High School,and Toffee. The routine is ended abruptly by an air raid siren, where everyone ducks under tables, and Jonny and Toffee fall in love. They begin dating, and end up going out for several months before Toffee's parents forbid her from seeing Jonny on the grounds that he is a bad person. She breaks up with him, and Jonny commits suicide by hurling himself into the Francis Gary Powers nuclear power plant. He is buried at sea in international waters with the rest of the nuclear waste.
Three weeks pass, and Toffee's peers begin to notice that she's been upset and is unable to focus on her baton twirling. She expresses her sadness over Jonny's death, and retells the night of Jonny's death from her point of view. Meanwhile, the rest of the school gets itself ready for the senior prom, which is rapidly approaching. Toffee continues to wear black clothing in mourning for Jonny. Her friends insist that she should go to Prom, and get over Jonny's death, since it's been "three whole weeks!"
Toffee begins to hear Jonny's voice on occasion. Her friends tell her, yet again, to move on from Jonny, but Toffee insists "he's dead, but he ain't gone." She gets frustrated and states that "life's a trap of the same old crap." 'Crap,' however, is a taboo word at Enrico Fermi High, and Miss Strict begins to discuss the philosophy of the school.
At school, much to her surprise, Toffee begins hearing Jonny's voice loudly from her locker. Jonny begs to be let free, and he bursts from the locker, shocking the other students. His reappearance is not well-received, and the students are scared and disgusted by Jonny's deteriorating appearance.
Not to miss out on a story, reporter Eddie Flagrante picks up on the story from Josh, a cub reporter from Enrico Fermi High.
Trying to cope with Jonny's unexpected reappearance, Toffee talks with him about what brought him back. As it turns out, a voice he heard, saying "Jonny, I love you so" brought him back. It's revealed that the voice was Toffee. Inspired to come back to school, Jonny returns ready to graduate. Miss Strict, however, has different plans. She does not approve of zombies and refuses to let him return to school. Jonny has had a change of heart and appreciates the wisdom of what Miss Strict teaches. Even so, she refuses to let him return.
Toffee is not certain what to do. She confers with her friends, who believe that she should not have to take Jonny back. Jonny's friends, on the other hand, believe that if she still loves Jonny, she should take him back. Toffee ends up rejecting Jonny. Josh points out Jonny to Eddie, who recognises Miss Strict. They proceed to argue over Jonny's rights and end up in a stalemate. Flagrante believes Jonny should return, while Miss Strict believes the school rule on zombies should be enforced: "Rule Number 7, Subsection 9, of the handbook of student life, says: No zombies, no zombies!" After the end of their discussion, Act I ends.
The students at Enrico Fermi High school have begun to believe Jonny should be let back into school. Some students put up posters and fliers, and Miss Strict elects to cancel the pep squad, to the dismay of the students. Not slowed by her tactics, the students continue to protest and begin to disobey the dress code. Miss Strict dismantles the baseball team. Even so, the students go on, and make a petition to reinstate Jonny as a student. Strict puts all seniors on probation, and threatens to cancel all after-school events. She also promises that at the next sign of rebellion, she will cancel the senior prom.
Eddie has continued with the Jonny Warner story. During a commercial break, Eddie Flagrante asks for the number to Our Lady of Divine Masochism, a Catholic Orphanage. The reason is unknown. He interviews Jonny about what he plans to do. Jonny goes on to explain that he cannot give up love because it is what brought him back. He goes as far as to propose to Toffee on national TV.
Meanwhile, Toffee can't keep focussed on her schoolwork. She debates with herself if she should take back Jonny. Her friends, Candy, Coco, and Ginger, call on a party line and talk with her about her situation. None of them missed Jonny's TV appearance, which was broadcast on "all three channels." In the end, Toffee chooses to take Jonny back.
Flagrante tracks down Miss Strict and begins flirting with her. It is revealed that they were lovers in high school, and had a very physical relationship. The last time they were together, as Miss Strict says, was in the back seat of Eddie's father's Studebaker. They discuss their relationships in art class, Glee Club, and French class. At the end of the song, they both sing how the other had left them, but no specifics are revealed.
Prom night arrives. The students marvel at how the school has been decorated for the prom. Toffee approaches Jonny, and tells him that she'll always be with him. They dance and continue to discuss their love for each other.
Jonny's appearance at prom did not go unnoticed by Miss Strict. She halts the music and the prom when she calls him out for being there. Eddie appears in order to confront Miss Strict with her secrets. Being questioned on why she hates Jonny Warner, she replies, "No comment." The prom is cancelled. Pushed by Flagrante, Miss Strict tells the students her past. As it turns out, she and Eddie conceived a child on the night of their senior prom, but it was taken away as soon as it was born, and she never knew who it was. Eddie, who had done some digging, reveals that Jonny is her long-lost son. Overjoyed at the discovery, Miss Strict allows the prom to continue, and Toffee and Jonny get to do one more dance before the curtain drops.
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