Dr. Elena Kinder (Kathleen Turner) is out to dominate the world. Two-year-old Sly is the only person in her way. Dr. Kinder and her partner in crime, Dr. Heep (Christopher Lloyd), have a covert research lab dedicated to cracking the code to a secret baby language. When Sly escapes from the lab, he joins his twin brother Whit in an effort to expose the nefarious plot. Raised by his uncle (Peter MacNicol), who cares for special children, Whit is naive to the ways of the world, and is quickly captured by Dr. Kinder. Mistaken for Whit, Sly is taken back to his uncle, where he rallies the other foster babies into a Super commando rescue squad to invade the secret lab in an effort to squash Dr. Kinder's evil plot.