Playing around while aboard a cruise ship, the Chipmunks and Chipettes accidentally go overboard and end up marooned in a tropical paradise. They discover their new turf is not as deserted as it seems. For a vacation, Dave and the Chipmunks (Alvin, Simon and Theodore) and Chipettes (Brittany, Jeanette and Eleanor) go on a cruise ship. The Chipmunks and the Chipettes end up creating trouble. Dave notices that his old boss, Ian Hawke is working as the ship's safety monitor dressed as a pelican, and is out to inform the captain if the Chipmunks and Chipettes cause more problems. Alvin goes para-sailing on a kite, but the kite flies away with him and the other Chipmunks. Dave goes on a hang-glider to find them but Ian stops him, and they both end up in the Pacific Ocean.

The world famous singing pre-teen chipmunk trio return to contend with the pressures of school, celebrity, and a rival female music group known as The Chipettes. After a concert mishap lands Dave in the hospital, Alvin, Simon, and Theodore end up in the care of Dave's twenty-something cousin Toby. When the Chipmunks put aside their stardom to return to school to win a annual "Battle of the Bands" competition to save the school's music program. But the boys meet their match with the Chipettes, Brittany, Jeanette, & Eleanor, who are working for the Chipmunks's ex-manager Ian Hawke. Romantic sparks and crazy mishaps happen when the Chipmunks and Chipettes square off.

A struggling songwriter named Dave Seville finds success when he comes across a trio of singing chipmunks: mischievous leader Alvin, brainy Simon, and chubby, impressionable Theodore. In a tree farm, three musically inclined chipmunks, Alvin, Simon and Theodore, find their tree cut down and sent to Los Angeles. Once there, they meet the frustrated songwriter David Seville, and despite a poor house wrecking first impression, they impress him with their singing talent. Seeing the opportunity for success, both human and chipmunks make a pact for them to sing his songs. While that ambition proves a frustrating struggle with the difficult trio, the dream does come true after all. However, that success presents its own trials as their unscrupulous record executive, Ian Hawke, plans to break up this family to exploit the boys. Can Dave and the Chipmunks discover what they really value amid the superficial glamor around them?