Two scientists, Dr. Elena Kinder (Kathleen Turner) and Dr. Heep (Christopher Lloyd), use genius-baby studies to fund BabyCo's theme park "Joyworld". According to Dr. Kinder's research on toddlers/babies, babies are born possessing vast, universal knowledge and speak a secret yet impossible-to-translate baby pre-language called ''Babytalk''. However, at age 2–3, the knowledge and language are lost as the babies ''cross over'' by learning how to speak human languages. Most of the babies raised in Dr. Kinder's underground research facility were adopted from the Pasadena City orphanage, transformed into little geniuses through use of the Kinder Method, and then used in experiments to decipher this secret yet impossible-to-translate language used by the 7 baby-geniuses.
The film starts with a group of babies in a day care center. Archie tells his friends, Finkleman, Alex, and Rosita, a story about Kahuna; according to Archie, Kahuna is a super baby with super strength and seemingly doesn't age, and he once rescued a group of children from an evil orphanage at the Berlin Wall run by a villainous overseer Kane.
When valuable objects begin disappearing throughout Europe, it's up to a band of brilliant babies to travel overseas and catch the thieves before it's too late.