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An evil scientist named Ian Hawke captures an ordinary family of chipmunks and mutates them, giving them humanlike appearance, increased intelligence, and extraordinary powers, such as super strength and flight, now given the names Alvin, Simon and Theodore. However, Hawke demands the chipmunks help his quest for world domination, but headstrong Alvin had other ideas. They break out of Ian's lab and end up in the custody of a comic book writer named Dave Seville. From then on the chipmunks use their powers to fight Ian's mutant's and stop him from conquering the world. Eventually Ian decides to match the chipmunks by cloning them, however a slight malfunction turns them into the female chipettes, Brittany, Jeanette, and Eleanor, with powers that match the chipmunks. Ian convinces the chipettes that the chipmunks are the enemy and they fight off the chipmunks, until the chipettes find out Ian's true intentions and become the chipmunks allies.  

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