In a nearby breeding ground, a Carnotaurus triggers a stampede which forces an Iguanodon mother to abandon her nest. One surviving egg journeys through several terrains before landing on a faraway island populated by prehistoric lemurs. Plio, the daughter of their patriarch Yar, names the hatched baby Aladar and raises him as her adopted son, despite Yar’s initial objections.

Years later, a fully grown Aladar and the lemurs take part in a mating ritual, where his friend Zini (Plio’s younger brother) is unable to achieve a mate. Moments after the ritual ends, they are interrupted when a gigantic meteor crashes into the Earth, creating an explosion-like tsunami that destroys the island and annihilates all the lemurs. However, Aladar, along with the lemurs, flee and survive by leaping into the sea towards the mainland. They look back at their ruined home and mourn for the loss of their loved ones before deciding to move on.

While crossing deserted wastelands, the group are attacked by a pack of Velociraptors. After escaping from them, the family encounter a massive herd of dinosaurs led by two Iguanodons named Kron and his lieutenant Bruton who are on a journey to the “Nesting Grounds”. After the herd rest for the night, Aladar and the lemurs befriend Baylene, an elderly Brachiosaurus; her friend Eema, a Styracosaurus; and Url, her dog-like pet Ankylosaurus. The next morning, the herd reach a seemingly dried lake which they have relied on for past trips. Kron orders the herd to move on until Aladar and his friends discover water lying under the surface, thereby saving the herd from dehydration.

Later that evening, Kron’s sister Neera, impressed by Aladar, begins to grow closer to him. Meanwhile, two Carnotaurus follow the herd’s tracks and begin hunting them for food. Bruton and an Iguanodon scout named Creto search for water, but are attacked by the Carnotaurus. Bruton manages to escape, but Creto is killed and eaten by the Carnotaurus. Bruton warns Kron, at which point he evacuates the herd, leaving Aladar, the lemurs, and the elderly dinosaurs behind while the Carnotaurus are in pursuit.

During a night storm, the group encounter Bruton, who was left behind by Kron, before taking shelter in a cave. Shortly after, the Carnotaurus enter the cave and attack the group, but Bruton sacrifices himself as he fights off the dinosaurs. Aladar and his friends escape and venture deeper into the cave, but they reach a dead end of piled rock. They smash through the dead end and arrive at the Nesting Grounds on the other side. While exploring, Eema finds a large wall of boulders blocking the original entrance to the valley.

Realizing that the herd will never make it, Aladar rushes off alone to rescue them, although he is pursued by the Carnotaurus along the way. Aladar soon catches up with Kron, Neera, and the herd and suggests a safer way to the valley, but Kron selfishly refuses to listen. Kron loses his temper and attacks, but Neera stops her brother from killing Aladar and comes to the latter’s aid. The herd eventually turns against Kron and abandons him, deciding to let Aladar lead them to the Nesting Grounds via the safer way.

As they prepare to leave, Aladar, Neera, and the herd find themselves cornered by the Carnotaurus. However, Aladar rallies Neera and the herd to stand together and they drive the predator back. The Carnotaurus chases after Kron who attempts to climb the cliff. When Kron reaches a sheer drop, he realizes that Aladar was right and tries to defend himself against the Carnotaurus. As it prepares to finish Kron off, Neera saves her brother, but is quickly overwhelmed. Aladar then fights the Carnotaurus until the cliff underneath breaks apart, sending the predator plummeting to its death. Kron dies from his wounds.

As their new leader, Aladar now leads the herd to the Nesting Grounds. Sometime later, a new breed of dinosaurs hatch; among them are Aladar’s and Neera’s children. The lemurs find more of their kind and the group all begin a new life together in their new home.