Two scientists, Dr. Elena Kinder (Diane Keaton) and Dr. Heep (Christopher Lloyd), use genius-baby studies to fund BabyCo's theme park "Joyworld". According Dr. Kinder's Research, babies are supposed to possess vast, universal knowledge and speak a secret yet impossible-to-translate baby prelanguage called "Babytalk". At age two, however, the knowledge and language are lost as the babies "cross over" by learning how to talk. Most of the babies that were raised in Dr. Kinder's vast, underground research facility were adopted from the Pasadena orphanage, transformed into geniuses through use of the Kinder Method, and then used in experiments to decipher the language used by the baby-geniuses. One mischievous toddler, Sylvester (AKA Sly), makes repeated attempts to escape Dr. Kinder's research facility and one night, Sylvester goes into a dirty diaper truck and he actually succeeds. The next morning, one things Sylvester does not expect is to run into his twin, Whit, in a mall playground. Although Sylvester and Whit share a telepathic bond, they have no idea of each other's existence. While the guards from Dr. Kinder's research facility capture Whit, mistake him for Sylvester, and take him back to Dr. Kinder's research facility, Sylvester is taken home by Whit's adopted mother, Robin (Kim Cattrall), who is Dr. Kinder's niece. After Dr. Kinder is horrified that Whit and Sylvester switched at the mall, she decides to do a cross evaluation on Sylvester and Whit. However, when she comes to Dan Bobbin's place, she realizes that Dan Bobbin can understand babies. After the attempts to retrieve Sylvester fail, Dr. Kinder decides to move the research facility to Lichtenstein, so that they can transform Whit into becoming a genius thanks to him getting bred by the Kinder Method (thus erasing his memories about his foster parents, foster brothers and foster sisters) and use him as an experiment to crack the code to "Babytalk". The babies at Bobbin's place hypnotize Lenny (Dom DeLuise), the bus driver to drive to Dr. Kinder's research facility. Once at the research facility, Sylvester goes to the control room to set the robots from the theme park on the lab scientists. When the Bobbins return home, their natural daughter Carrie tells her father that the children are in Dr. Kinder's research facility. At the end of the fight Dr. Kinder captures Whit and takes him to the helicopter pad on the roof. Robin and Dan chase them to the roof, where Dr. Kinder reveals that she and Robin are not related, and that Robin was adopted at age two. After Dr. Kinder got arrested by the police, Sylvester and Whit come together on the roof to cross over. Dan and Robin adopt Sylvester. Dan is still curious of the secrets of life, but as the twins have crossed over they no longer know those secrets. Carrie, their sister, doesn't reveal anything (just gives her dad a sly smile) because adults aren't meant to know their secrets.

Three pets set out across a wilderness to find their family and the children they love and miss.