In present-day New York City, an Eastern bluebird named Buster runs away from his siblings and he meets an intelligent orange Tyrannosaurus named Rex, who is playing golf. He explains to Buster that he was once a ravaging dinosaur, and proceeds to tell his personal story. In a prehistoric jungle, Rex is terrorizing other dinosaurs when a spaceship lands on Earth, piloted by an alien named Vorb. Vorb captures Rex and gives him "Brain Grain", a breakfast cereal that anthropomorphizes Rex and vastly increases his intelligence. Rex is introduced to other dinosaurs, altered by the Brain Grain: a blue Triceratops named Woog, a purple Pteranodon named Elsa, and a green Parasaurolophus named Dweeb. They soon meet Vorb's employer Captain Neweyes, the inventor of Brain Grain, who reveals his goal of allowing the children of the present time to see real dinosaurs. He plans to take them to Dr. Julia Bleeb who will guide them to the Museum of Natural History, and warns them to keep away from Professor Screweyes, his nefarious and evil brother who travels around causing mischief after losing his left eye several years ago. Neweyes drops the dinosaurs off in the Hudson River in the present day, but they are unable to meet with Bleeb. Instead, they meet a young boy named Louie, who plans on running away to join the circus. Louie agrees to help the dinosaurs get to the museum. Riding on Elsa, Louie soon encounters a girl named Cecilia, who is miserable with her life because of her neglectful parents. She agrees to run away with Louie and help the dinosaurs, and when she threw away her Thanksgiving hat, it lands on a little girl who wished for a similar hat and ends up granting her wish. To prevent mass panic, Louie decides that the dinosaurs need to stay hidden during their journey to the museum. He disguises them as floats in the Macy's Thanksgiving Day Parade. But when Rex sees the Apatosaurus balloon coming out in the parade, Rex naively greets it, thinking it is real and already intelligent like he is. Then in the process of hand-shaking, Rex unwittingly punctures the balloon, causing it to run out of air and fall on the dinosaurs, but left them unharmed. When the audience realize that live dinosaurs are among them, they fly into a panic, and the dinosaurs flee to Central Park while being pursued by the police and the army. Meanwhile, Louie and Cecilia meet Professor Screweyes, who is running his "Eccentric Circus". Unaware of Screweyes' sinister nature, the children sign a contract to perform in his circus troupe. When the dinosaurs arrive at the circus, Screweyes explains that he delights in scaring people and believes that the dinosaurs would make a great addition to his circus. Using his "Brain Drain", pills that are the polar opposite of his brother's Brain Grain, Screweyes devolves Louie and Cecilia into chimpanzees. When he offers the dinosaurs to consume the pills and join his circus as a ransom in exchange for the two children's freedom, they reluctantly accept and Screweyes releases Louie and Cecilia, agreeing to tear up their contract in the process. Knowing their friendship will be lost forever, Rex transforms Louie and Cecilia back to their human forms with his gentle pats. And before leaving, he sadly tells the two children to remember him. As the kids awake the next morning, they are greeted by a circus clown named Stubbs, who works for Professor Screweyes, serves them breakfast and explains everything. Upon seeing the dinosaurs returned to their natural savage states, Louie and Cecilia plan to sneak into the night's show and save the dinosaurs with Stubbs' help. That night, Professor Screweyes opens his circus with a parade of demons and evil spirits, and then unveils the dinosaurs to the terrified audience. Screweyes says he can control Rex, and proceeds to hypnotize him, while bragging that he is never afraid. However, a crow unintentionally activates the flare lights, breaking Rex out of the trance. Realizing he has been tricked, Rex becomes enraged and attempts to eat Screweyes, making him afraid after his talk. However, Louie steps in and desperately talks Rex out of killing Screweyes. His impassioned pleas and loving touches, along with Cecilia's, return Rex and the other dinosaurs to their kind and friendly natures. Just then, Captain Neweyes arrives in his ship and congratulates Louie and Cecilia, who proceed to kiss, while Stubbs puts on an act announcing his resignation from Professor Screweyes' employ which wins the audience over with laughter. Neweyes, Louie, Cecilia and the dinosaurs board the aircraft, leaving Screweyes to be swarmed upon and devoured by the crows and one crow flies off with his now powerless screw. The dinosaurs spend the rest of their days in the museum, allowing children to see live dinosaurs, and thus fulfilling their wishes. Back in the present, Rex tells Buster that he and his fellow dinosaurs are still in the museum. He also reveals that Louie and Cecilia have reconciled with their respective parents and become a couple. Rex returns Buster to his family, ignoring his brothers' taunts while hugging his mom, and Rex tells him to remember his story before leaving for the museum