Telly Paretta (Julianne Moore) believes that her son, Sam (Christopher Kovaleski), died fourteen months ago in a plane crash, but her husband Jim (Anthony Edwards) tells her that she's delusional and that they have never had a son and even her best friend Eliot (Jessica Hecht) doesn't appear to believe in Sam's existence despite her closeness to him. Dr. Munce (Gary Sinise) tells her that Sam was merely a figment of her imagination and is just imagining a life that might have been. He recommends that she be sent to a hospital, but she runs away and meets with a man named Ash (Dominic West) who she thinks is the father of a girl (Kathryn Faughnan) who was friends with her son and died in the same crash. At first he dismisses her, claiming he never had a daughter, and calls the police. After she is taken into custody, however, he remembers his daughter and rescues Telly. Together they escape and go into hiding, pursued by National Security agents. Telly and Ash capture an agent (Lee Tergesen), whom they threaten. The agent reluctantly reveals that he and other agents are merely helping "them" and that they do so to protect humankind. The roof of the house blows off and the agent, along with the roof, is sucked into the sky — presumably taken by "them"- and Telly and Ash flee. Eventually, Telly visits Dr. Munce again and he reveals that the disappearances are the work of "them," and that the government monitors their trials, all too aware that they have no power to stop "them" from doing whatever they want. Doctor Munce takes Telly to an airport and the dilapidated hangar of Quest Airlines, where he introduces her to an agent of “them” (Linus Roache). He tells the agent that “It’s over,” and to stop the experiment because it will only cause more harm. The agent replies, saying “It’s not over,” and then tells Telly that she has been a part of an experiment to test whether the bonds between mother and child can be diminished. In her case, her memories could not be erased. Telly refuses to deny her son's existence. The agent mentions that if he fails to erase her memory then he will look like a failure. The agent then subdues her and finally succeeds in erasing her memories of her son. During further questioning, though, a question about the name of her son triggers Telly's memory of her pregnancy, and all of her memories of Sam return. This causes the agent to be "abducted" himself, supposedly for his failure to erase her memory. This ends the experiment. Telly finds herself living a normal life, although she remembers everything that has happened. She reunites with Sam at a park. Also at the park is Ash, watching over his daughter. Like Sam, he has no memory of what has happened. Telly reintroduces herself, and the two sit and watch the kids play in the playground.

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.