During the Chipmunks' benefit concert in Paris, Dave Seville (Jason Lee) suffers a severe injury, when Alvin (Justin Long) jumps on top of a scaffolding and a falling billboard sends Dave flying across the stage into some electric devices. After the accident, he is rushed to the hospital. Although he survives, he must stay for a few days to recover, so he leaves his lazy 21-year-old cousin Toby (Zachary Levi) and Aunt Jackie (Kathryn Joosten) in charge of the Chipmunks until he returns. Prior to the event, Dave had made arrangements for Alvin, Simon (Matthew Gray Gubler), and Theodore (Jesse McCartney) to go to school. But, at the airport, Aunt Jackie falls down some stairs and an airport luggage trolley crashes into her. She has to go to the hospital too, so Toby is left in charge. Little does Dave know, on their first day at school, the Chipmunks feel uncomfortable with all the bullies around, when Ryan, one of the bullies, gives Simon a swirlie. The boys have fun being babysat by Toby, mainly because he is basically a big kid himself. Theodore tries to bond with Toby but Toby is always either ignoring him or being short towards him.

Meanwhile, Ian Hawke (David Cross) the greedy soundtrack-editor now lives in the basement of Jett Records. But, a FedEx mail comes to the building and a package falls out. And, three singing female chipmunks, The Chipettes, Brittany (Christina Applegate), Jeanette (Anna Faris), and Eleanor (Amy Poehler) come out of the package, and introduce themselves. Brittany says that since Ian made the Chipmunks stars, they want to be stars too. So they sing "Put Your Records On" to make Ian adopt them. He does, telling them that the Chipmunks ran away from him, spat on him, and left him broken-hearted, to make the Chipettes not trust them. He lets the Chipettes stay in his apartment (in actuality, breaking into a model suite) and have their own dressing mirrors. Meanwhile, the Chipmunks enter the school concert to win $25,000 and save the school's music program. The tension between Alvin and Simon continues to build as Alvin hangs out with the jocks of the school, but the one who is most affected is Theodore who believes he is losing his brothers with them fighting all the time. The Chipmunks meet the Chipettes and fall in love, until they discover they're with Ian. The Chipettes sing "Hot N Cold" to get Dr. Rubin (Wendie Malick), the school principal to enter them in the contest. The Chipmunks and the Chipettes compete against each other in a Battle of the Bands. Alvin warns Brittany about what Ian did to him and his brothers, but she doesn't believe Alvin. Alvin then humiliates Simon in front of everyone when he tells one of the jocks to trick him into thinking he's now the school Litter Moniter and Simon ends up being thrown into the dumpster. Meanwhile, Ian gives Eleanor some platform shoes, telling her to "work on being taller." At the concert, the Chipettes sing "Single Ladies (Put a Ring on It)." Eager to get rich, Ian videotapes the Chipettes performance and posts it on YouTube, along with his phone number. The Chipettes win after Simon and Theodore forfeit the competition because Alvin failed to show up (he hung out with the football team instead). Finally, Alvin shows up only to see that everyone's gone. Brittany says to Alvin that he doesn't care about anyone but himself and that she never wanted to win the way Ian was making her. When Alvin returns home, Simon and Theodore pretend they're sleeping and ignore him. The embarrassment is too much for Theodore to take who runs away to the zoo, hoping to live with the meerkats, after seeing Meerkat Manor. When Toby and the boys find him and save him from an eagle, it brings out the best in all of them and the Chipmunks all forgive each other and go back to "One for all, and three for one". (As Theodore put it)
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