Act One

A toxic waste dump. Two men, one black and one white, emerge to setup the stage – we are in a place between heaven and hell, filled with filthy air and dark despair: Tromaville, New Jersey. The cast gradually enters to join the two dudes and everyone wonders who will save them from this hellhole ("Who Will Save New Jersey?"). Enter Melvin Ferd, III, a very nerdy scientist with environmental tendencies. Unfortunately, he's not exactly the savior type. The two dudes sum up the situation.

Melvin goes to visit the Tromaville Library, where he finds Sarah, a beautiful blind girl that he is in love with. Melvin has figured out that a corporation named The Good Earth is responsible for polluting Tromaville; if he could find the town records, he could save Tromaville. Luckily, the records are in the library. As Melvin goes to get them, two jocks, Bozo and Sluggo enter, and begin giving Sarah a hard time. In the course of trying to defend her, Melvin inadvertently reveals that he's in love with Sarah.

In the Mayor's office, Mayor Babs Belgoody is scheming with two waste management executives so that she can elevate her political career and become governor ("Jersey Girl"). Melvin enters and threatens the Mayor with his newfound knowledge: that she owns The Good Earth company. He says he'll go to the media, but she makes a deal with him and offers to hire him as his deputy ("Jersey Girl – Reprise"). Melvin is thrilled. After he leaves, the Mayor summons Sluggo and Bozo to stop Melvin ("Get the Geek"). The bullies find Melvin by the toxic waste dump, where he is trying to save Tromaville. They dump him into a vat of goo. As they're about to flee the scene, Sarah appears. The bullies intercept her and threaten her ("Get the Chick / Get the Geek – Reprise"). Just as they are about to have their way with her, Melvin transforms into a superhero,  the Toxic Avenger, and comes to her rescue. He rips the bullies to pieces ("Kick Your Ass"). Melvin promises Sarah (who is unaware that the person who saved her is Melvin) that the bullies will never bother her again, but she is concerned that he used violence. Melvin lies and says he did not use violence. The police arrive to clean up the crime scene ("Who Will Save New Jersey? – Reprise").

In Sarah's apartment, she wonders who her strange savior is. Afraid that she will discover he is a monster, Melvin treads lightly on the topic, and a misunderstanding occurs. Sarah believes that Melvin is a Frenchman named Toxie. Sarah is relieved that Toxie did not use violence on the bullies, and he promises her that he will never hurt a soul ("Promise"). Before leaving, he agrees to come back for brunch the next day. Sarah rejoices in her newfound love, calling her best friends to tell them all about it ("My Big French Boyfriend").

As Toxie walks home, he revels in the fact that Sarah is interested in him, despite his grotesque features ("Thank God She's Blind"). On the way, he sees a thug beating up a little old lady, but he refuses to intervene and use violence. Eventually, though, he can't resist helping her and he rips the mugger's arm off and beats him up with it. When he gets home, Melvin's mother has been waiting up for him. She is very disappointed in him for having turned into a monster ("Disappointment"). Nevertheless, she gives him the insurance card so he can go to the doctor.

Toxie sees the doctor, who cannot figure out what is wrong with him and sends him to Professor Ken, "the best scientific mind in Tromaville." Professor Ken doesn't have any method of reversing the transformation; he just warns Toxie to stay away from household bleach.

Back at her apartment, Sarah has an idea for a new novel she can write, one that's based on her romance with Toxie. When Toxie comes over for brunch, he deftly tries to keep her from discovering his true nature. He also admits his inexperience with love, and she admits her experience. As they bond over small things, Toxie professes his love for Sarah, and she responds in kind ("Hot Toxic Love"). Just as she is about to kiss him, a foghorn blows and he has to leave – he's afraid the next shipment is coming in.

At the Tromaville docks, more barrels of toxic waste are being unloaded. Toxie confronts the Mayor and promises to expose the evil she has done. The Mayor is enraged and accuses him of trying to become a folk hero. A folk singer enters and details how the citizenry has warmed up to this odd hero ("The Legend of the Toxic Avenger").

The Mayor visits Professor Ken in his laundry room and seduces him into helping her fight Toxie. Despite his reservations, they have been together before, and he finds her impossible to resist ("Evil Is Hot"). Professor Ken then reveals that Toxie can be killed with common household bleach.

Lorenzo is at the Tromaville Beauty Salon ("Who Will Save New Jersey? – Reprise 2"). Melvin's mother, Ma, is lamenting about the heartache and trouble that her son has brought her. Lorenzo warns her that the Mayor is on her way to get Ma. This is very bad; Ma and the Mayor cannot be in the same room at the same time... as they are played by the same actor. The Mayor arrives, and Ma runs into the broom closet. A farcical argument ensues between the broom closet and the beauty salon as the women hurl insults at each other ("Bitch/Slut/Liar/Whore").

Act Two

Sarah finishes her manuscript and knows that there's only one person who can help her make this dream a reality: Oprah ("Choose Me, Oprah"). Fresh from the shower, Toxie enters Sarah's living room and notices her sexy dress, although he keeps his distance. Sarah can't understand why they've been together for so long and yet, nothing physical has happened. The Mayor comes on via loudspeaker and commands the citizens of Tromaville to assemble at City Hall with all of their bleach. Toxie realizes that he is in danger and tells Sarah that he needs to leave town. The Mayor and Sal the Cop arrive at Sarah's apartment; they reveal to her that Toxie is a freak, not a Frenchman. When they leave, Toxie returns and confirms that their story is true, allowing her to feel his face ("Hot Toxic Love – Reprise"). He also reveals that he is Melvin, and Sarah rejects him. Toxie is extremely angry; he has been played for a fool and he has no allies, so he plans to take no prisoners ("Death Promise"). He terrorizes people on the street and kills an old woman. When he sees a sweet couple together, he breaks down from his heartache ("You Tore My Heart Out").

Sarah is at the Tromaville Coffee Shop, pouring her heart out to her best friends, Diane and Shinequa. Ma finds Sarah there and tells her that Toxie is on a rampage because of her. Sarah is upset, but can't get over her revulsion to Toxie's looks. Ma tells her that this is the burden every woman shares – there are no great men ("All Men Are Freaks"). Sarah is convinced.

On the steps of City Hall, the Mayor is mobilizing a lynch mob against Toxie, the terrorist who killed an old woman ("Till the Monster's Dead"). The cops chase Toxie through the streets of Tromaville, with Sarah close behind, trying to save him... until she runs into a wall. Eventually, the Mayor catches him and is about to cover him in bleach, saying the name of the woman he killed, in the process: Edna Ferbert. Suddenly, Sarah intervenes – this is wonderful news! Edna Ferbert was a horrible woman, and everyone is better off now that she is dead! ("Hot Toxic Love – Reprise 2"). The Mayor comes at Toxie and Sarah, but Sarah shoots her. As she dies, she spills bleach on Toxie, who crumples to the ground and dies, as well ("Hot Toxic Love – Reprise 3").

Professor Ken rushes in, only to discover that he is too late. ...Or is he? There is a remote possibility of a cure: drinking a vile and disgusting liquid. It works, and Toxie is saved! Sarah asks Toxie to marry her ("Promise – Reprise"). Toxie shares a vision that he had "when he was dead," about how to save New Jersey ("A Brand New Day in New Jersey"). The townspeople are thrilled and celebrate with Toxie being named governor and the introduction of Toxie Jr.