For a vacation, Dave (Jason Lee) and the Chipmunks (Alvin, Simon and Theodore) (Justin Long, Matthew Gray Gubler and Jesse McCartney) go on a cruise ship. The Chipmunks and Chipettes (Brittany, Jeanette and Eleanor) (Christina Applegate, Anna Faris and Amy Poehler) turn the ship into their personal playground causing trouble and running amok as they will. Dave notices that his old boss, Ian Hawke (David Cross) is working as a safety monitor on the cruise. Alvin goes para-sailing on a kite and he flies away with the other chipmunks. Dave goes on a hang glider to find them with Ian and they both end up in the ocean around Hawaii.

Meanwhile, the six chipmunks find an island and they sleep for the night. Dave enlists Ian’s help to find the same island and begin looking for the six chipmunks…