Theodore encounters a stray kitten that entered through an open window in the house. He and the boys take an instant liking to the kitten, and after some compromising, they name the kitten Cookie Chomper III, and after Dave is cured of his allergy to cats, he comes to like the kitten as well. After Cookie Chomper gets run over, the boys have a hard time dealing with it. Eventually, they get a new pet, a puppy they name Lilly.

Alvin lies to his classmates that he will be singing on stage with Michael Jackson. As Alvin tries to find Michael in order to see if it really is possible he could perform with him, he meets up with the big star's manager. To Alvin's surprise, this so-called manager is a homeless man looking to find a place to stay.

The Chipmunks overhear Dave suggesting that he would prefer Alvin to be a Gymnastic Pizza Twirler, Simon a Pogo Stick Tester, and Theodore an iguana trainer, and immediately start to pursue those careers.

The boys disobey Dave and instead of seeing a kid's movie, they go in and see a horror movie. The movie ends up scaring the Chipmunks out of their wits. All night, the boys think that Hideous Harold, the creature from the horror film, is after them.

Simon is frustrated being the smartest member of the family. He invents a cap that helps Dave and his brothers become smarter. Simon is so confident with his family’s new smarts that he signs them up to be on a genius game show. But before he could give his family another boost of the thinking cap, he loses it.

Alvin is desperate to write an essay on George Washington, that he uses Simon's time machine to bring George into the future.

Simon makes a video of his family for his class project. Unfortunately for Dave and his brothers he took the video in not their greatest moments, and is nervous when Simon’s video will air on TV.

Alvin is tired of being treated like a kid and trades place with Dave for a day to feel what it is like to be a grown-up.

Alvin tampers with Simon's hair growth formula and instead having it grow Simon's hair, it turns him into a heartthrob.

Dave gets a bump on the head and forgets who he is. After seeing a commercial, Dave becomes a trendy stylish man.

The Chipettes are excited for the summer holidays, but not when Miss Miller keeps making other plans for them. The girls decide to hook her up with an elderly man by the name of Mr. Flowers.

Alvin has a dream that he is a detective from the 40s. He is on a case to find a famous rich girl named Brittany.

The Chipettes discover the joys of writing in a diary. Tension builds between them when they deliberately sneak a peak at what the other Chipette has written.

All three boys find themselves having a crush on the science substitute teacher. In order to impress her, they each make a project for the science fair.

The Chipmunks decide to have a family reunion with their aunts and uncle, but things are not well between them. Each Chipmunk finds out that the three of them have issues and believes many years ago each of them tried to sabotage the other in their chosen carriers.

The boys are accidentally shrunk by one of Simon's inventions. They end up going inside Dave's head in order to try telling him what happened.

The Chipmunks and Chipettes participate in the school journalism. They end up covering the story of "Sleeping Beauty". During the investigation, Brittany pricks her finger on the spin wheel and becomes cursed, just like the real story.

The boys are fed up with their puppy's antics and set out to train Lilly to behave. But soon the Chipmunks feel they are not qualified to raise her and they give her away.

The janitor gets a chance to sing on stage.

Cruise leads to the Fountain of Youth.

Brittany works at a farm.

Alvin, as usual, is thinking of himself when it comes around to being Christmas. He is so focused on receiving presents that he fails to think of poor Mr. Carroll, who just wants his morning paper. Will the spirits of Christmas past, present, and future help Alvin learn the error of his ways?