The film opens with an Iguanodon mother forced to abandon her nest, with only one egg surviving a Carnotaurus attack. The egg eventually ends up in an island inhabited by Smilodectes, who see the egg hatch, name the baby dinosaur Aladar, and raise him as their own. When Aladar is an adult, he meet Jimmy, Carl, Sheen, Cindy, Libby, Goddard, The ICarly Gang, The P.C.A Gang, Sonic, Tails, Knuckles, Amy, Sticks, Scrooge McDuck, Hewey, Dewey, Louie, Gizmoduck, Webby, Darkwing Duck, Lauchpad McQuack, Gosalyn Mallard, Honker Muddlefoot, Tank, Herb & Binkie Muddlefoot (Honker's Family), Morgana McCawber, Steggmutt, Neptunia, Dudley Puppy, Kitty Katswell, The Chief, Keswick, Basil, Dr. Dawson, Olivia Flaversham, Chip, Dale, Gadaget, Monterey Jack, Zipper, The Powerpuff Girls, Skunk, Panda, Fox, Rabbit, Mrs. Bird, Tiger, Warthog, Bird, Woody, Buzz and their gang, The McCloud Patrol, Peter Pan, Wendy, John, Michael, The Lost Boys, Jake, Izzy, Cubby, Orson, Roy, Wade, Booker, Sheldon, Bo, Lanolin, and the Phineas and Ferb Gang. Later, the island is destroyed when an asteroid crashes on Earth, causing a violent meteor shower, with only Aladar, his grandfather Yar, his mother Plio, his best friend Zini and his sister Suri surviving the destruction of the island by swimming to the mainland.
After fleeing a pack of Velociraptor, the family meets a multi-species herd of dinosaurs (consisting of a bunch of Iguanodon, Styracosaurus, Pachyrhinosaurus, Stygimoloch, Microceratops, Parasaurolophus, and Struthiomimus) led by the Iguanodon Kron and his lieutenant Bruton the Altirhinus, who are on a journey to reach the "Nesting Grounds", a valley believed to be untouched by the devastation of the asteroid impact. Aladar, the lemurs befriend and our heroes a trio of elderly dinosaurs: Baylene the Brachiosaurus, Eema the Styracosaurus, and Url, Eema's dog-like pet Ankylosaurus. Aladar also develops romantic feelings for Kron's sister Neera, but she appears uninterested. Meanwhile, the Velociraptor pack continues to follow them, but are scared off when a pair of Carnotaurus (whom The League Of Villains, Beagle Boys, Magica DeSpell, The Fearsome Five, Steelbeak, Ammonia Pine, FOWL High Command, The Brainteasers, Camille Chameleon, Splatter Phoenix, Captain Hook, Mr. Smee, Orson's Brothers, The Weasel, Mojo Jojo, The Gangreen Gang, Dr. Doofansmirtz, and Fat Cat are working for) also pick up the herd's trail.
The herd arrives at a lake they have relied on for past trips, but it has dried up, due to the meteor shower from earlier. Aladar saves the herd from dehydration when he and Baylene eventually dig up the trapped water beneath the ground, though Kron claims the water for himself. Aladar and Neera eventually fall in love after Neera sees Aladar helping the dinosaurs (especially the elderly ones) survive. However, Bruton, having been sent by Kron to find water upon arrival at the lake, returns injured by the Carnotaurus which killed another Iguanodon that was scouting with him. Kron evacuates the herd from the lake bed in a rush, leaving Aladar, the lemurs, the elderly dinosaurs and the injured Bruton behind. When Aladar tries to slow the herd, Kron pushes him away and warns Aladar that he will be killed if he interferes with his leadership again. Neera wants to help Aladar but Kron forces Neera to leave him.
The small group recuperates in a cave during a rainstorm, with Bruton eventually befriending them. When the Carnotaurus, and the pair and villains attacks, Bruton proves his loyalty when he holds them off to ensure their escape and kills one of them as the others escape to the depths of the caves, dying in the process. Badly injured, the other Carnotaurus and the villains escapes, enraged by the death of its mate but unable to follow the group. Upon reaching a dead end, Aladar begins to lose hope, after repeated failures and the loss of Bruton. However, Zini smells fresh air, and finds the dead end to actually be a blocked exit that is hard to break down. His friends all join in breaking down the barrier, stabilizing his confidence. Finally, Baylene demolishes the wall. The exit actually leads to the "Nesting Grounds", although Eema sees that the old entrance – where the herd has gathered on the other side – has been blocked by a landslide generated by the meteors. Knowing that the herd will not survive the sheer drop from climbing over it, Aladar rushes to find the herd on the other side, accidentally alerting and being tracked by the Carnotaurus. He finds the herd being directed by Kron to climb the rocks, which cannot be passed without fatality, but when he suggests the alternate route he found, Kron becomes enraged at his authority being questioned and challenged, and attempts to kill Aladar to try and take back his leadership. Aladar is outclassed by Kron, who only stops short of killing Aladar when Neera, now fed up of her brother's illogical beliefs, strikes him down and defends Aladar, effectively desolving Kron's power as leader. Aladar and Neera take control of the herd, but Kron refuses to submit to the leadership of another and begins climbing the rocks himself.
The fight between Aladar and Kron proves to be a huge delay, as the Carnotaurus then confronts them, but Aladar rallies the herd to stand together against their longtime enemy. The Carnotaurus, overpowered, is forced to let the herd pass but spots Kron trying to climb the rocks alone and charges him as easy prey, followed by Neera and Aladar. In the ensuing fight, Kron is trapped at the edge of a precipice and severely wounded by the Carnotaurus, but Aladar is able to push the predator off the cliff to its death. Then Jimmy calls the police and arrest those villains for good. Kron, however, succumbs to his injuries and dies with Aladar and Neera at his side.
Aladar, our heroes and Neera lead the herd back to the "Nesting Grounds" through the cave, where the two eventually mate and have children, and the lemurs find more of their own kind. Plio narrates the ending, wishing for their story to be remembered in history. She then says, "But one thing is for sure. Our journey is not over, we can only hope in some small way our time here will be remembered".