One night, Littlefoot sees a strangely blue colored meteor falling from the sky and colliding into Threehorn Peak, a volcano 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. Littlefoot's friend Ducky overhears Pterano's plan, but Pterano and his cronies, Rinkus and Sierra, abduct her before she can warn the others. They take her along as they set out to find the Stone of Cold Fire.
The other dinosaurs discover Ducky's kidnapping. The adults tell the young ones 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 small, albino Sharpteeth. Pterano, a Pteranodon like Petrie, was able to fly away, although the event left him heart-broken. He ended up expelled from the herd as punishment for abandoning his followers.
Because the adults are slow to reach decision, Littlefoot, Petrie, and 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. After they find her, Ducky comforts Petrie, who is distraught about his uncle's actions, by stating that Pterano is the least wicked of the three Flyers, and that the potential for goodness still lives in him. Meanwhile, Sierra is showing mutionous feelings towards Pterano, and Rinkus convinces him to betray Pterano once they find the stone. 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 volcanos, the young ones manage to 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. Rinkus and Sierra have now discarded him and are attempting to get the stone to give them power. The volcano begins to erupt. In the nick of time Petrie's mother arrives with a friend to 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 exiled from the Great Valley and into the Mysterious Beyond for five years (to where Petrie says "five cold years" is so long and Mr. Threehorn says that some of the others think it must be a lot longer). Petrie tries to plead against the punishment. However, Pterano explains to him that everyone, including himself, must always take responsibility and be accountable for their own actions. Then after Petrie tells Pterano he will miss him, Mr. Threehorn imitates a sharptooth to scare him away.
That night, 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 flying rock he saw was a Stone of Cold Fire. The male Rainbow Face admits the flying rock wasn't, 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 starts to ask if there really is a Stone of Cold Fire and exactly who the Rainbow Faces really are yet they reiterate that "That would be telling wouldn't wouldn't it?" Littlefoot is momentarily distracted, and when he turns around, he finds a pillar of light where the Rainbow Faces stood. The light disappears, and a light flies across the sky before changing 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.
- Thomas Dekker .... Littlefoot
- Anndi McAfee .... Cera
- Aria Curzon .... Ducky
- Jeff Bennett .... Petrie / Spokes Dinosaur
- Rob Paulsen .... Spike / Rinkus
- Michael York .... Pterano
- Jim Cummings ... Sierra
- Kenneth Mars .... Grandpa Longneck
- Miriam Flynn .... Grandma Longneck
- John Ingle .... Cera's father
- Charles Kimbrough .... Rainbow Face #1
- Patti Deutsch .... Rainbow Face #2
- Tress MacNeille .... Ducky's Mom / Petrie's Mom
- Beyond the Mysterious Beyond - Rainbow Faces, Littlefoot, and Cera (Charles Kimbrough, B. J. Ward, Thomas Dekker, and Anndi McAfee)
- Good Inside - Ducky, Petrie, Cera, Littlefoot and Spike (Aria Noelle Curzon, Jeff Bennett, Anndi McAfee, Thomas Dekker and Rob Paulsen)
- Very Important Creature - Pterano, Rinkus and Sierra (Michael York, Rob Paulsen and Jim Cummings)
"If We Hold On Together" (instrumental)
Home video release history
- December 5, 2000 (VHS and DVD)
- December 4, 2001 (VHS and DVD)
- December 2, 2003 (VHS and DVD - 4 Movie Dino Pack (Volume 2) and 9 Movie Dino Pack)
- November 29, 2005 (DVD - 2 Mysteries Beyond the Great Valley)