After a Carnotaurus ambushes an infant Parasaurolophus, the stampede of the dinosaurs causes an Iguanodon mother to abandon her nest. The one surviving egg journeys through several predicaments via the flight of a Pteranodon, before ending up on a far away island populated by lemurs. A lemur named Plio names the hatched baby Aladar and raises him. Years later, Aladar and the lemurs take part in the mating ritual, where Plio’s brother Zini goes without a mate. Moments after the ritual ends, a meteor strikes and destroys the island. Aladar, Plio, Zini, their father Yar and Plio’s daughter Suri flee and jump across the sea to the mainland. They mourn for the loss of all lemurs before moving on.
While wandering across deserted lands, they are ambushed by a pack of Velociraptor. After escaping from them, the family come across a remaining multi-species herd of dinosaurs led by Kron and Bruton, who are on a journey to reach the “Nesting Grounds”, a valley said to be untouched by the devastation of the meteor. Aladar and the lemurs befriend a trio of elderly dinosaurs, Baylene, Eema and Url along the way. Together with the herd they migrate, eventually reaching a lake they have relied on for past trips. Though it has seemingly dried up by the meteor, Aladar and Baylene discover the water being buried under the dried surface of the lake and saves the herd from dehydration. Impressed by Aladar’s compassionate ways, Kron’s sister Neera begins to fall in love with him. Meanwhile, a pair of Carnotaurus picks up the herd’s trail and begins stalking them for food. During a scouting mission, Bruton is attacked and wounded by the predators. He escapes and returns to inform Kron that they are being followed, sending the entire herd in grave danger. Kron picks up the pace and evacuates the herd, leaving Aladar’s family and Bruton behind, while the Carnotaurus are in pursuit some distance away.
During a rainstorm, the stragglers spend the night in a nearby cave before being found and attacked by the beasts. Bruton sacrifices himself to cause a cave-in that kills him and one of the Carnotaurus. As the rest of the group move through the cave, one Carnotaurus survives and resumes its search for the herd. Aladar loses hope when they reach a dead end, but the others convince him to keep going, relating how he inspired them to do the same. After they knock down the dead end together and successfully find the Nesting Grounds on the other side, Eema sees a large wall of rocks from a landslide that blocked the original entryway to the valley. Knowing that the herd will die climbing over it, Aladar rushes off alone to find them, before being pursued by the Carnotaurus.
Aladar catches up with the herd and suggests a safer way into the valley, but Kron angrily fights him. Neera stops Kron and the herd decides to abandon him, taking Aladar as their new leader. As they prepare to leave, they are cornered by the Carnotaurus. Aladar rallies the herd to stand together and scare off the predator, but it senses and follows Kron on the cliff. Aladar and Neera fight back against the Carnotaurus, as it kills Kron. After Aladar knocks the Carnotaurus off the cliff to its death, he and Neera mourns for his demise.
The herd are then led back to the Nesting Grounds as their new home. Sometime later, a new generation of dinosaurs hatches, among them are Aladar and Neera’s children. The lemurs finds more of their kind, and soon they begin embarking on a new life together.