Near the end of the Cretaceous era, an Iguanodon mother is forced to abandon her nest during a Carnotaurus attack. The one surviving egg journeys through several predicaments, before ending up on an island populated by lemurs, where an Iguanodon baby hatches and is adopted by Plio, who names it Aladar. Years later after growing up, Aladar and the lemurs takes part in a mating season, where Zini is left without a mate. Soon after it ends, a meteor strikes and destroys the island, leaving Aladar, Plio, Yar, Zini and Suri, as the only survivors when they are alone escape to the mainland. The family mourns for the loss of all lemurs before moving on.
While crossing a deserted wasteland, 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, providing sanctuary. Aladar and the lemurs befriend a trio of elderly dinosaurs, Baylene, Eema and Url, along the way. Together, they migrate with the herd for miles, eventually reaching a lake they have relied upon in past trips. Though the lake 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, 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, unknown to the others. During the scouting mission, Bruton is attacked and injured by the predators, before he escapes and returns to inform Kron that they are being followed, sending the entire herd into a panicked flurry. 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.
The stragglers spend the night in a nearby cave during the rainstorm. Soon, they are found and attacked by the beasts. Bruton sacrifices himself to cause a cave-in that kills him and one of the Carnotaurus in the process. While the rest of the group pushes on deeper into the cave, one Carnotaurus survives, roars in anger 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 the other entryway to the valley being blocked by a large wall of rocks from a landslide. Knowing that the herd will die climbing over it, Aladar returns to the desert alone and is pursued by the Carnotaurus.
When he catches up and prevents the herd from getting over the cliff during the monster's approach, he suggests a safer way to the valley. Kron angrily challenges and attempts to kill Aladar, but Neera stops Kron. The herd accepts Aladar as their replacement leader, but they are cornered when the Carnotaurus arrives. Aladar rallies the herd to stand together and scare off the predator, who then goes after Kron on a cliff. Neera and Aladar fight back against the Carnotaurus, when it overwhelms and fatally wounds Kron. After Aladar knocks the Carnotaurus off a cliff to its death, Kron dies from his injuries, with Aladar and Neera at his side.
Aladar and Neera lead the herd back to the Nesting Grounds, where the lemurs have found more of their own kind and the new generation of dinosaurs hatches sometime later, along with Aladar and Neera's children.
- The Griffin Family (Peter Griffin, Lois Griffin, Meg Griffin, Chris Griffin, and Stewie Griffin), Vinny Griffin, Glenn Quagmire, Cleveland Brown, Joe Swanson, Little Bear, Duck, Cat, Owl, Hen, Emily, Lucy, Natsu Dragneel, Lucy Heartfilia, Gray Fullbuster, Erza Scarlet, Wendy Marvell, Happy, Carla, Sheeta, Pazu, The Crystal Prep Girls, Blythe Baxter, Zoe Trent, Pepper Clark, Penny Ling, Sunil Nevla, Vinnie Terrio, Minka Mark, Russell Ferguson, Doug Funnie, and Skeeter Valentine guest star in this film.
- Atlantis: The Lost Empire, Doug's 1st Movie, and Dinosaur are all Disney films. While Laputa: Castle in the Sky is disturbed by Disney which also made Dinosaur.
- Inner Sanctum/The Attack
- The Egg Travels/Lemur Island
- Playing monster
- The Courtship
- The Meteor strikes!
- Raptor attack/Aladar and our heroes join the herd/Meeting Baylene, Eema, and Url
- Crossing the desert
- Finding water/Carnotaur ambush
- Aladar and Neera/Left behind
- The misfits, and our heroes find Bruton/In the cave
- The Carnotaur attack!/Bruton's sacrifice
- Back to the herd/The Nesting Grounds!
- Aladar and Kron's fight
- Stand together/The final fight
- Happy ending