In an alternate timeline, the asteroid that wiped out the dinosaurs passes the Earth. Millions of years later, two Apatosaurus farmers named Henry and Ida give birth to three children; Libby, Buck, and their youngest, Arlo. While his siblings adjust to their responsibilities, signified by elaving their mud print on their corn silo, Arlo's timidness causes him to make his tasks difficult.
Henry makes Arlo guard the crops from a feral caveboy who is stealing them, but the caveboy flees into a ravine. Arlo and Henry follow it, but a flash flood occures, and Henry sacrifices himself to save Arlo. Some time later, Arlo spots the caveboy and pursues it to a river, where they both plummet underwater. Waking up, Arlo finds himself far away from home. The caveboy, who Arlo dubs 'Spot', makes attempts to befriend Arlo, giving him berries and defending him from a snake. A Styracosaurus named Forrest Woodbush is impressed and declares that Spot will accompany Arlo to his home. As the two journey together, they bond, and Spot reveals that his parents had died.
The following morning, Arlo and Spot are attacked by a group of Pterosaurs led by Thunderclap, but they are rescued by a family of Tyrannosaurs consisting of Butch and his children, Ramsey and Natch. Arlo and Spot help the Tyrannosaurs locate their herd and defend them from a pack of Velociraptors. The Tyrannosaurs are impressed and help the two find their way to the area of their homeland. Along the way, Arlo and Spot notice a caveman, but ignore him. However, as they near Arlo's home, the Pterosaurs return and abduct Spot. Arlo, invigorated by a vision of his father, resolves to rescue Spot. Arlo battles Thunderclap and his group and manages to defeat them, but he and Spot plummet down a waterfall.
Arlo and Spot survive and venture to Arlo's farm, where they meet a family of cavemen. Arlo allows the cavemen to adopt Spot, and the two bid farewell before Arlo returns to the farm and reunites with his family. Arlo is allowed to then leave his mud print on the corn silo.
- Raymond Ochoa as Arlo.
- Jack Bright as Spot.
- Sam Elliot as Butch.
- Anna Paquin as Ramsey.
- A.J. Buckley as Nash.
- Jeffrey Wright as Poppa Henry.
- Frances McDormand as Momma Ida.
- Marcus Scribner as Buck.
- Maleah Padilla as Libby.
- Steve Zahn as Thunderclap.
- Peter Sohn as Forrest Woodbush.