One night, Littlefoot, a young dinosaur, sees a strangely colored "flying rock" falling from the sky and colliding with a mountain in the Smoking Mountain range. When Littlefoot describes it the next morning, most of the adult dinosaurs in the Great Valley disbelieve Littlefoot's story. However, two newcomers, the mysterious "Rainbow Faces", speak eloquently of possibilities of wonders beyond what they know. The Rainbow Faces suggest the rock may be a "Stone of Cold Fire", a stone possessing magical properties. Pterano, the devious, sinister and outcast uncle of Littlefoot's friend Petrie, overhears the conversation and conspires to use the rock to take control of the Great Valley. Pterano asks Petrie, who idolizes him, for the location of the rock and is told it has landed on Threehorn Peak, a volcano. Littlefoot's friend Ducky overhears Pterano's plan, but Pterano, his cronies, Rinkus and Sierra, The Dazzlings, Diamond Tiara and Silver Spoon, and Diesel 10 abduct the before she can warn the others. They take them along as they set out to find the Stone of Cold Fire.
The other dinosaurs discover Ducky and Sue's kidnapping. The adults tell the young ones and Tino and the others that Pterano had been made an outcast due to his carelessness after self-appointing himself leader of a group of dinosaurs; While searching for the Great Valley after an earthquake Pterano was overconfident and led his followers directly into a pack of Sharpteeth Deinonychus dinosaurs. Pterano, a Flyer like Petrie, was able to fly away but was expelled from the herd as punishment for abandoning his followers.
Because the adults are slow to reach decision, Littlefoot, Petrie, Tino, Doraemon, Thomas, Twilight, their friends, Cera and Spike take off by themselves in search of Ducky, who, meanwhile, falls through the floor into a cave while running from the flyers and the villains. After they find them, Ducky comforts Petrie, who is distraught about his uncle's actions, by stating that Pterano was the least wicked of the three Flyers, and that the potential for goodness still lives in him. The young ones pursue the Flyers, hoping to reach the Stone of Cold Fire before them. Aided by the Rainbow Faces, who suddenly appear and offer their knowledge of volcanoes, the young ones manage arrive at Threehorn Peak before the Flyers. They discover that the Stone is an ordinary meteorite. Lamenting over this realization, Pterano states that he had meant to create a paradise with the power of the stone, not realizing that this paradise already exists in the form of the Great Valley. The volcano begins to erupt. In the nick of time Petrie's mother and her friend evacuate the young dinosaurs, leaving Rinkus and Sierra behind where they are caught in the explosion of the Stone. Pterano is thanked for saving Ducky but as punishment for his plan Pterano is banished from the Great Valley and into the Mysterious Beyond for five years.
Littlefoot finds the Rainbow Faces and asks them when they are leaving. A meteor flies overhead, and the female comments, "Any time now". Littlefoot, somewhat unnerved, asks the Rainbow Faces whether the Stone of Cold Fire is actually real. The male Rainbow Face admits the stone does not exist, but explains that the young ones' effort to search for it was what really mattered. The Rainbow Faces reiterate their claim that there are many unknowns to be discovered "beyond the Mysterious Beyond". Littlefoot is momentarily distracted, and the Rainbow Faces disappear. In their place is a crystalline pillar of light, which shimmers briefly and vanishes. As it goes, a meteor streaking across the sky suddenly changes its course, flying upward and off into the night. Littlefoot's friends find him and Littlefoot, inspired by the Rainbow Faces, reflects that there are many unknowns and that such unknowns make life wonderful.
- Twilight Sparkle, Applejack, Rarity, Rainbow Dash, Pinkie Pie, Fluttershy, Spike (MLP), The Cutie Mark Crusaders (Apple Bloom, Sweetie Belle and Scootaloo), Thomas the Tank Engine, Percy, Diesel 10, The Dazzlings, Diamond Tiara and Silver Spoon guest stars in this film.
- Diesel 10, The Dazzlings, Diamond Tiara and Silver Spoon will work for Pterano.
- Jason Marsden as Tino Tonitini
- Grey DeLisle as Lor McQuarrie
- Phil LaMarr as Carver Descartes
- Kate Soucie as Tish Katsufrakis
- Mona Marshall as Doraemon
- Johnny Yong Bosch as Noby Nobi
- Cassandra Morris as Sue
- Brian Beacock as Sneech
- Kaiji Tang as Takeshi "Big G" Goda
- Rebecca Shoichet as Sunset Shimmer
- Joseph May as Thomas the Tank Engine
- Christopher Ragland as Percy
- Tara Strong as Twilight Sparkle
- Ashleigh Ball as Rainbow Dash / Applejack
- Andrea Libman as Pinkie Pie / Fluttershy
- Tabitha St. Germain as Rarity
- Cathy Weseluck as Spike the Dragon
- Michelle Creber as Apple Bloom
- Claire Corlett as Sweetie Belle
- Madeleine Peters as Scootaloo
- Thomas Dekker as Littlefoot
- Anndi McAfee as Cera
- Aria Curzon as Ducky
- Jeff Bennett as Petrie / Spokes Dinosaur
- Michael York as Pterano
- Rob Paulsen as Rinkus/ Spike
- Jim Cummings as Sierra
- Kenneth Mars as Grandpa Longneck
- Miriam Flynn as Grandma Longneck
- John Ingle as Cera's father
- Tress MacNeille as Ducky's Mom / Petrie's Mom
- Charles Kimbrough as Rainbow Face #1
- Patti Deutsch as Rainbow Face #2