After Professor Screweyes cons Louie and Cecilia into signing up as employees of his circus, the dinosaurs agree to take the Professor’s Brain Drain and become primal again in exchange for the kids’ freedom.
When Screweyes exhibits them at his show the next night, he puts Rex under hypnosis. However, his hypnotic hold soon gets broken, causing Rex to get a hold of him with intent to eat him. Louie rushes up to Rex and begs him to let Screweyes go, saying that he didn’t need to be this primal beast. At the same time, Cecilia wishes for “no bad happen.” Louie’s pleas reach Rex and turn him back to his intelligent self. Louie and Cecilia then hug the others, causing them to go back to their intelligent selves, too.
Then, Captain Neweyes arrives in his airship, having heard Cecilia’s wish on his wish radio. Louie and Cecilia kiss, and Stubbs tells Screweyes (comedically) that he’s quitting his circus. Screweyes refuses Neweyes’ offer to forsake his evil ways and come with him, so Neweyes, Louie, Cecilia, and the dinosaurs leave in the airship. Screweyes is now all alone, and his fear overcomes him. The flock of crows that always hung around the circus proceed to flock to him and cover his entire body. When they disperse, all that remains is his screw eye, which another crow picks up and flies off with.
The dinosaurs are taken to the museum and finally meet Dr. Bleeb. She arranges an exhibit where the dinosaurs pose as statues while the parents are around, but once the parents leave, they come alive for the kids, fulfilling their wishes to see real dinosaurs.
In the epilogue, Rex tells Buster that Louie and Cecilia became a couple, and they both made up with their parents. Buster gets Rex’s point and thus returns to his family. Rex then heads on back to the museum, where he and the others still live.