For a vacation, Dave (Jason Lee) and the Chipmunks (Alvin, Simon and Theodore) (Justin Long, Matthew Gray Gubler and Jesse McCartney) and Chipettes (Brittany, Jeanette and Eleanor) (Christina Applegate, Anna Faris and Amy Poehler) go on a cruise ship. The Chipmunks and the Chipettes end up creating trouble. Dave notices that his old boss, Ian Hawke (David Cross) 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.
Meanwhile, the 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 Chipmunks. The next morning, the Chipmunks go and find food and while doing so, an island castaway named Zoe (Jenny Slate) shows up and sees the Chipmunks and Chipettes for the first time. They then go to Zoe’s tree house where Eleanor sprains her ankle and Simon gets bitten by a spider, the side effects including personality changes and loss of inhibition.
The morning after, everyone observes Simon’s personality has changed and he has no memory of being Simon; he also thinks he is a French, adventurous chipmunk named Simone (Alan Tudyk). “Simone” becomes attracted to Jeanette but does not take as kindly to Alvin and Brittany. Later, Zoe takes Simone, Jeanette, Eleanor and Theodore to a lake with a waterfall and Simone finds a cave. He returns with a gold bracelet which he gives to Jeanette as a crown. Brittany and Alvin see an active volcano the next day and they decide that they have to leave the island with the others. Theodore and “Simone” find Dave and Ian and they go to meet with the other chipmunks. They all begin to prepare a raft to get them off the island and everyone is assigned a job. When Jeanette and “Simone” go and look for food, “Simone” is knocked unconscious and Jeanette is kidnapped; “Simone” reverts to Simon afterwards.
Everyone finds Simon awake and he cannot remember anything since the bite. They discover that Zoe has taken Jeanette and they head towards the waterfall. When they approached the tree log to cross, Dave and Alvin decide they’ll go and find Jeanette. As Zoe forces Jeanette to get the treasure in the cave by tying her to a rope, Alvin and Dave come to her rescue. The island begins to rumble again and Zoe lets go of the rope and Jeanette runs with Dave and Alvin back to the raft. When they reach the log to cross, Dave almost falls.
Alvin and Ian convince Zoe to help save Dave. They then run towards the raft and escape the eruption. While on the raft, Zoe apologizes to Jeanette for kidnapping her and forcing her to get the treasure. As a gift, Jeanette gives Zoe the gold bracelet that Simon had given to her. Alvin reconciles with Dave and they are rescued. The Chipmunks and Chipettes perform at the International Music Awards. Ian also starts a new career as a screenwriter by selling a screenplay about Zoe’s story to Hollywood, earning him his wealth back.
In a post-credits scene, the Chipmunks, the Chipettes, and Dave are on a plane heading back home. Alvin is speaking on the pilot’s microphone and tricks the passengers into thinking that the plane’s destination is set for Timbuktu. He accidentally pushes the food cart, and it hits Dave, leading him to shouting his trademark yell, “ALLLLVINNN!!”, once more.