Littlefoot, a young apatosaurus, is still living with his friends Cera, Ducky, Petrie, Spike, Chomper and Ruby in the Great Valley. His father Bron and a cowardly Nothronychus named Wild Arms are now living in the Valley. Wild Arms is supposed to be looking after Chomper that day, but is too scared of the baby Sharptooth and lets him run off. Chomper chases an insect off into the Mysterious Beyond and then realises he is lost. He can’t find his way back and runs around frightened. However, Chomper does not see the Velociraptor known as Screech watching him from a distance. Screech then runs off to tell his boss Red Claw (a scarred Tyrannosaurus) and his ally Thud, about this victim. Littlefoot then hears from Wild Arms about the disappearance of Chomper. He is shocked, but believes the Grown ups will think that it is too dangerous. Littlefoot finds Shorty, a young Brachiosaurus and asks him to come with them. Shorty isn’t interested at first, but goes when he is reminded that Chomper helped save his life once, and is told he can boss around the others. Littlefoot and his friends sneak off to find Chomper without the adults knowing. Wild Arms reluctantly goes with them too.
The gang make their way into the Mysterious Beyond and wander through a desert. However, the gang are attacked by Screech, who is on his way to tell Red Claw about Chomper. The gang fights off Screech, knocking him down. Red Claw and Thud then arrive at that moment. While the gang hides, Screech tells Red Claw and Thud what he saw. The gang sneaks off while Screech is chatting. Then the gang ends up in a path full of herbs. Spike then eats the herbs in their way, allowing the dinosaurs to pass through. Suddenly they are attacked by a red Tarbosaurus. Wild Arms runs away in fear. Shorty gets cocky and tries to fight the brute, but it strikes him with its tail. Then the other members of the gang each pull off several attacks on the Tarbosaurus. Littlefoot lures it away from Shorty, Spike and Cera push a rock onto its head, Ruby and Littlefoot start throwing fruit at the beast, while Petrie pecks it in the eye. All these attacks are useless and the Tarbosaurus chases the gang. Suddenly a Therizinosaurus appears and fights the brute. While the Tarbosaurus is occupied, the Prehistoric Pals jump into a lake, where it can’t follow them. The Therizinosaurus joins them. Meanwhile, Ducky swims to the bottom of the lake and chews through some vines, which makes logs float to the surface, creating a path. The Therizinosaurus introduces herself as Amber. She explains she knew the kid’s teacher Mr.Thicknose and he told her all about them. Meanwhile, Shorty is upset that Littlefoot wouldn’t let him fight the Tarbosaurus and decides to abandon him. Shorty leaves with Cera, Ruby, Ducky, Petrie and Spike (much to their annoyance) while Littlefoot is left with Amber. Amber tries to cheer him up, but they are attacked by Red Claw, Screech and Thud. Amber quickly uses her claws to scare off the predators, and she and Littlefoot go off to find Shorty and Chomper.
Shorty and the rest of the gang are climbing a volcanic mountain, since they have heard Chomper screaming at the top. However falling rocks roll down the mountain and a pack of hungry Deinonychus attacks the gang. The gang still makes it to the top, where Littlefoot and Amber join them. They find Chomper and Amber chases the Deinonychus away. But the gang still has to get down. They use a large leaf to sled down the mountain. As they head home through the desert, the Tarbosaurus appears, along with Red Claw, Screech, Thud and the remaining Deinonychus. Amber is taken out by the Tarbosaurus, which then fights Red Claw for the food. Back at the Great Valley, Wild Arms find Bron, Grandpa Longneck and the rest of the adults, and tells them where the little ones are. The grown ups rush to the desert and fight the Sharpteeth. Mr.Threehorn, Grandpa Longneck, Mr.Thicknose and Ducky’s mother fight off Red Claw, Screech Thud and the Deinonychus, while Bron sends the Tarbosaurus plummeting off a cliff to its death. Amber is thought to be dead, but it turns out she is actually alive. The dinosaurs all head back to the Great valley, and Chomper promises only to play safely in the Great Valley.
Felix Avitia as Littlefoot Anndi McAfee as Cera Aria Noelle Curzon as Ducky Jeff Bennet as Petrie Rob Paulson as Spike Damon Wayans Jr. as Wild Arms Nancy Cartwright as Shorty Naomi Scott as Amber Isaac Brown as Chomper Meghan Strange as Ruby and Ducky’s Mother Jim Cummings as Grandpa Longneck Scott Whyte as Bron Miriam Flynn as Grandma Longneck George Ball as Daddy Topps Dorian Harewood as Mr. Thicknose