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An oracle warns the queen of Planet Woodius that an evil scientist called Dr. Hawke will take over the kingdom, and the only way to stop him is to separate her three sons, wait until they grow up, and reunite with them to overthrow Hawke. She does so, leaves them each with a magical amulet that transforms into an instrument-like weapon for self-defense, and goes into hiding. Alvin was misplaced and was found by a gang of thieves who taught him street smarts, Simon was raised by a rich family who give him a high education, and Theodore was raised by a suburban foster family with many children. The queens oracle reunites them and tells them of the prophecy. Ever since the chipmunks sought to find clues that lead to their mothers hiding place, and avoid Dr. Hawke's bounty hunters. On the way they meet three orphaned girls called the chipettes, after the oracle made them amulets similar to the chipmunks they become the chipmunks occasional allies.

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