A paleontologist named Zack takes his nephew Ricky and niece Jade on a fossil hunt. While alone, Ricky is met by a talking raven, who turns into an Alexornis named Alex. He tells him of a story set in the Cretaceous period 70 million years ago. Patchi is the smallest in a litter of Pachyrhinosaurus hatchlings, and is often bullied by his older brother Scowler. Their father Bulldust is the leader of the Pachyrhinosaurus herd. Alex, who is Patchi's mentor, tries to help Patchi impress a female Pachyrhinosaurus named Juniper, but her herd migrates south without him. Patchi is also attacked by a Troodon which attempts to take him away but is saved by Bulldust, resulting in Patchi having a hole in his frill as an injury which Alex claims that Patchi was "destined for greatness".
Bulldust moves his herd south as well, but when they try to pass through a forest, they are forced to flee when a storm strikes and a fire erupts. Taking advantage of the chaos, a pack of Gorgosaurus attacks the scattered herd. They kill the rest of Patchi and Scowler's family while their leader Gorgon fights and kills Bulldust, who had been trying to protect Patchi and Scowler. Afterwards, Patchi's herd (now led by Bulldust's rival Major) combines with Juniper's as they continue their migration. There, Gorgon's pack attacks them again. In the ensuing chaos, Patchi, Scowler, and Juniper fall into a river and are swept downstream to the ocean, with Alex following them from above. At a beach, Scowler follows a herd of Edmontosaurus to find food, callously leaving Patchi and Juniper behind. The two make their way through a forest and eventually are able to find their herd and Scowler.
After years of making the same migration from north to south and vice versa, an adult Scowler becomes the herd's new leader after defeating Major, and chooses Juniper to be his mate, much to Patchi's disappointment. Scowler recklessly leads the herd onto a frozen lake, but Patchi is able to lead the majority of the herd to safety. Enraged and believing Patchi to be usurping him and also trying to take Juniper from him, Scowler confronts Patchi and challenges him for a battle in exchange for leadership of the herd. Scowler quickly gains the upper hand and wins as he disowns Patchi before ordering Juniper and the rest of the herd to leave him as well as Alex behind. Despondent and heartbroken, Patchi, who had gotten trapped under a tree during the fight, tries to allow predators to kill him, but Alex convinces him to die for something worth dying for as Bulldust did.
Reinvigorated by the advice, Patchi escapes and fights off the predators, before returning to the herd, only to find them under attack by Gorgon and his pack again. As Gorgon overpowers him in battle, a repentant Scowler orders Patchi to save himself and lead the herd to safety. Instead, Patchi leads them into fighting off Gorgon and his pack. The herd successfully forces the Gorgosaurus pack to back off while Patchi defeats Gorgon by breaking his arm which had gotten caught in the hole in Patchi's frill, saving Scowler. Scowler reconciles with Patchi and then concedes leadership of the herd to him, while Patchi goes on to have eggs with Juniper, one of which hatches and Alex asks for it to be named after him. In the present day, moved by Alex's story, Ricky returns the Gorgosaurus tooth to Zack and Jade, who have discovered Gorgon's skull buried in the ground.
Justin Long ... Patchi
Tiya Sircar ... Juniper
John Leguizamo ... Alex
Skyler Stone ... Scowler
Karl Urban ... Uncle Zack
Charlie Rowe ... Ricky
Angourie Rice ... Jade