In an alternate history, the asteroid that would have caused the extinction of the dinosaurs 65 million years ago passes safely over Earth. Millions of years later, Apatosaurus corn farmers Henry and Ida have three children: Libby, Buck, and Arlo. While his successful siblings are allowed to "make their mark" (a mud-print on the family's corn silo), Arlo's timid nature makes tasks difficult for him. Henry attempts to give Arlo a sense of purpose by putting him in charge of guarding their silo and helps him set a trap. It captures a caveboy, but Arlo cannot bring himself to kill him and sets him free. Disappointed, Henry takes Arlo to track the caveboy, leading them into a ravine. Henry saves Arlo from a flash flood before being swept away and killed.
Without his father, Arlo shoulders more of the workload. He spots the same caveboy inside the silo and, blaming him for his father's death, chases him into a river, where he hits his head on a stone and is knocked unconscious. Awakening, he finds himself far from home and tries to survive on his own, but becomes trapped when a boulder pins his leg. The next day, Arlo wakes to find his leg has been freed, and the caveboy appears with food for him. The caveboy then leads Arlo to a berry tree, where the caveboy fends off a large snake, amazing Arlo, and impressing Forrest Woodbush, a nearby eccentric Styracosaurus who wants to keep the boy. He forces Arlo to compete with him to give the boy a name he will respond to, which Arlo finally wins when he calls him "Spot". Arlo and Spot bond as Arlo laments his lost family, and Spot reveals that his parents are dead.
Later, when a storm strikes, Arlo runs away in fear and loses the riverbank he has been following home. The next morning, Arlo wakes to find Spot at his side. They are noticed by a band of pteranodons, led by Thunderclap, who appear to be conducting a rescue operation but turn out to be savagely carnivorous. When the pterodactyls try to take Spot, Arlo and Spot flee, happening upon a pair of Tyrannosaurus named Nash and Ramsey, who ward off the pterodactyls. Nash, Ramsey, and their father Butch have lost their herd of longhorns, so Arlo offers Spot's help in sniffing them out.