A troupe of actors in Victorian costume addresses the audience ("Dr. Jekyll & Mr. Hyde"). They tell the story of Dr. Jekyll, a good and decent scientist who invented a potion to turn himself into the murderous Mr. Hyde, and who died as a result of his dangerous experimentation.

But there's another story to be told. Henry Meckler, a high school student, reads Dr. Jekyll and Mr. Hyde and becomes obsessed with it. Henry is a straight-A student and president of the chemistry club, but he can't talk to Chelsea McFadden, the girl he has a crush on. His best (and only) friend, Stuart, advises him to make up lies to impress her (he's a champion surfer, raised in Africa). But, when Henry decides to march right up to her and ask her out, he's intercepted by Chuck Vernicker, the class bully, who robs and humiliates him in front of Chelsea... just like every other day.

But today, Henry vows to change things by changing himself. He tells Stuart that he's going to recreate Dr. Jekyll's formula ("What If..."). After all, if a person is only chemicals, why not alter a few of those chemicals a bit? Stuart tells Henry that he's crazy, but Henry withdraws into his garage laboratory. For weeks, he hides not only from his family, but from Stuart, who is tormented by an alcoholic father and desperately needs his best friend's ear, and reminds Henry of his promise never to tell anybody else about it. Meanwhile, Henry finishes his potion, drinks and... nothing happens.

Despondent, Henry joins his ever-patient parents and his squabbling brother and sister at the dinner table ("Just Once"). As Tony and Beth scream and carry on, their parents urge them to be more like quiet, obedient Henry. But, in the middle of his father telling about his day at the bank, Henry begins to change ("Something's Happening"). He runs from the room.

The next day at school, everybody's gossiping about the handsome, confident "New Kid." Chelsea and her friend, Marissa, flirt with him. Even Stuart doesn't recognize him, and he introduces himself as Eddie. Eddie faces down Chuck and stops him from bullying Stuart. He intimidates his teacher, Mr. Hebner, into letting him into history class and stands up and asks Chelsea out in front of everybody. She says yes. Eddie is everybody's hero.

But Stuart is worried about Henry, wondering why his friend missed school for the first time ever. But Henry was there, and he proves it by recounting the events of the day to Stuart. Then, he reveals his secret: he drinks his potion and turns into Eddie ("More"). He feels great and he pressures Stuart to join him. Stuart declines, first politely and then more firmly. Eddie starts to threaten Stuart, then changes his mind: "If you don't want any, that just leaves me more."

Coming out of a movie with Chelsea that Friday night, Eddie starts spinning all of Stuart's lies about surfing and Africa. In the middle of a story about his pet elephant, Spot, he starts to turn back into Henry. He takes more of his potion in front of Chelsea, placating her by saying that it's medicine for a rare, non-contagious disease that he got in Africa.

Eddie takes over more and more of Henry's life ("More – Sequence"). Stuart finds Eddie to be no substitute for his best friend, and Henry's teachers worry about the effect that his new attendance problem will have on the chemistry scholarship for which he is applying. Eddie even bullies Chelsea into getting out of a weekend with her grandmother to spend more time with him.

Henry's parents get a letter from Henry's school and confront him, but he refuses to answer their questions, angrily asserting his independence ("Something's Wrong").

Transformed again, Eddie tries to convince Stuart, Chelsea and Marissa to help him steal a car so that they can go to the beach for the weekend and "borrow" somebody's beach house. Stuart finally stands up to Eddie and refuses to go. Eddie retaliates by telling the girls about Stuart's alcoholic father. Stuart storms off, and so does Marissa. Chelsea tries to follow them, but Eddie yells, begs and physically threatens Chelsea, grabbing her wrist so hard that it hurts. She promises to go with him that weekend, and he turns sweet and nice again.

Later that day, Henry reverts to himself and begs Stuart for forgiveness, but Stuart recognizes the signs of addiction ("More – Reprise"), and tells Henry to get help. Henry insists that he's got it under control and that he can stop on his own.

To prove it, he decides to talk to Chelsea as himself, not as Eddie. He tells her that Eddie has gone away and is never coming back... and is surprised to find her relieved. They find that they have more in common than they thought, since Chelsea wishes that she were smart, like Henry, just as much as Henry wishes he were popular, like her ("If I Were You"). Henry hesitantly asks her out, and – to their mutual astonishment – she agrees. It looks like Eddie is gone for good.

But, Henry still has to get through his interview for the chemistry scholarship and he still has a vial of potion in his pocket, even though he had sworn off it. As he waits, getting more and more nervous, he finally succumbs and drinks the potion. He transforms into Eddie, who insults the interviewer, tears up Henry's application essay and goes to find Chelsea. He calls her stupid and threatens her again, but she's had enough this time. She walks out on him, leaving him shouting after her.

Eddie runs back to his lab, desperate for his next fix. Henry's mother walks in and doesn't recognize her own son. She comes between Eddie and the beaker of potion, tries to kick him out and threatens to call the police. Then, Eddie comes down, transforming back into Henry in front of her eyes. He attacks her, wanting only the potion, and realizes only too late what he's done. Finally, at rock bottom, he recognizes that he can't stop and asks her for help. The rest of the cast joins her in assuring Henry, "You're Not Alone."