After watching many horror films, Alvin Seville is plagued by nightmares of meeting the Wolfman. He confides in Simon Seville and Dave Seville that their new neighbor, Mr. Lawrence Talbot, seems to be hiding a monstrous secret. When Alvin triggers an experimental accident at the school auditorium, and when Dave receives a call from Miss Miller about the Chipettes being frightened by a mysterious presence while walking home with the Chipmunks one night, Dave and Principal Milliken decide that Alvin should be pulled from his role as Mr. Hyde in the school’s production of Dr. Jekyll and Mr. Hyde. To shore up his confidence, Theodore steps in as Mr. Hyde, and Dave confiscates Alvin’s monster collection.
To help boost Alvin’s self-esteem, Theodore steps into the role, while the typically shy Chipmunk struggles to keep up with the demanding performance. The rehearsal takes an eerie turn as the show’s events echo Alvin’s fears, and the tension between the kids and their enigmatic neighbor deepens. Dave’s decision to pull Alvin from the role creates a delicate balance at home and at school, setting the stage for a mystery that goes beyond a simple school play.
Alvin and Simon begin searching for proof that Mr. Lawrence Talbot is a werewolf. Meanwhile, [Theodore] has a moment of fate on his way home when he is bitten by what he believes to be a large dog after meeting his crush Eleanor. The next day at rehearsal, Theodore delivers a terrifying performance as Mr. Hyde to thunderous applause. He then starts transforming into a werewolf at night, while by day his personality shifts to a rude, sarcastic puppy-like demeanor. Realizing their brother is cursed with lycanthropy, Alvin and Simon pledge to find a cure and save the play without tipping off Dave. When their options run dry, they seek guidance from the eccentric psychic Madame Raya, who foresees a savage werewolf future for Theodore by the next full moon and urges them to act quickly.
Madame Raya suggests a drastic precaution: knock him unconscious with a silver weapon. Together, Alvin and Theodore hatch a risky plan. Alvin sneaks into Talbot’s home and steals his cane, topped with a silver wolf head. Theodore attempts to intervene, splitting the cane in two after Alvin knocks him on the head with it, but the curse remains active. As night falls, Dave tries to apologize to Talbot, hoping to ease the escalating danger. Talbot reveals that his cane’s head was forged from the silver bullets that killed his grandfather, and when Dave asks why he was attacked, Talbot begins to transform into a werewolf under the full moon. Dave rushes toward the school to warn the students but is knocked unconscious after colliding with a pole. Talbot makes his way inside and pursues Alvin.
During the school production, Theodore’s transformation becomes fully dangerous as he chases Eleanor. The crystal necklace Theodore gave Eleanor shines in the moonlight, triggering a memory of his true feelings for her and causing him to flee. Eleanor follows him, determined to help him, only to be nearly attacked by Mr. Talbot, whom the Chipmunks realize is the same werewolf who bit Theodore. The two brothers band together as the two werewolves clash; Theodore bites Talbot, and both revert to their human forms. Simon Seville explains to everyone how the bite effectively cured them by reversing the curse on both of them. With the danger temporarily behind them, Alvin Seville races to the stage to join the applause, and the crowd celebrates as if the entire incident had been part of the show.
At the wrap party, Talbot expresses gratitude to Theodore for freeing him from the family curse and announces his intention to succeed Principal Milliken as the new school principal, while she steps into a less stressful role, riding on rickety bridges in South America. The movie closes on a note of resolved tension and renewed purpose, with the Chipmunks and their friends navigating the aftermath of a night that looked like a monstrous crisis but turned out to be a life-changing lesson about trust, friendship, and the power of facing fears together.