One night, Littlefoot's Grandfather tells the protagonist children and Tino and the others a story about "The Lone Dinosaur", a legendary longneck who once protected the Great Valley from the most ferocious sharptooth ever to live. A fight ensued, which led to the Sharptooth's death. However, the sharptooth left "The Lone Dinosaur" with a scar slashed across his right eye. Soon after the battle, a huge monolith that resembled a proud sauropod, having life-sized tyrannosaur teeth arranged around his neck, came out of the ground during an earthquake. The dinosaurs called it "Saurus Rock". The legend also states that if anyone damages the monolith, bad luck would descend upon the valley.
A few days later when the kids are playing, Littlefoot accidentally falls off a cliff. Just before he hits the ground, a strange longneck dinosaur rescues him. This longneck introduces himself only as "Doc" and gives no knowledge of his history. Littlefoot is intrigued by this newcomer, who is scarred across one eye and displays prior knowledge of the Great Valley's topography.
For the preceding reasons, Littlefoot assumes that Doc is the Lone Dinosaur. He tells his friends this, narrating an apparently extemporaneous legend to support his assumption. Inspired, Cera's infant niece and nephew, the twins Dinah and Dana, go to Saurus Rock without anyone noticing. Later when the friends are playing, they notice that Dinah and Dana are missing. Recalling their talk of the day before, they go to Saurus Rock to find them.
When they finally reach Saurus Rock, they see Dinah and Dana on the top. As they climb up to rescue them, Dinah and Dana fall off the top and land on Cera, causing the life-sized stone tooth on which she is standing to break off.
As they walk home, an Allosaurus chases them. As they are pursuing it, they cross a gorge via through a suspended log. As the Allosaurus follows them, he throws the log over the ravine. They start to get out, and no sign of the Allosaurus yet, until Spike gets stuck though the gap in the log, and when he gets out, the Allosaurus breaks the log and falls into the ravine below.
When they get home, Cera is confronted by her father, who scolds her for losing the twins. Over the next few days, ill fortunes ranging from injuries to a tornado plague the valley. The adults blame Doc, in whose wake the misfortunes have apparently come, while Littlefoot blames himself and his friends, recalling the breaking of Saurus Rock.
Eager to prove himself a solitary hero, as great as the Lone Dinosaur (whom he idolizes), Littlefoot attempts alone to take one of the Allosaurus's teeth to replace the broken stone. He discovers, as he attempts to extract the tooth, that the Allosaurus is still alive. While he is running, he crawl between a large boulder that the Allosaurus is trying to break through, and Littlefoot is confronted by the most ferocious T-Rex that looks like it was from the story, and is almost eaten. Just as the T-Rex is near to him, he is rescued by his grandfather, who tells him to run as he finds his friends who lead his grandfather there. The T-Rex is then joined by the Allosaurus who broke through the boulder and are working together to take down his grandfather. The Allosaurus's leg is suddenly grabbed and pulled down by Doc's tail, who helps his grandfather. The two sharpteeth try to make a clear shot together, but hit the rock tower instead. The two elders then combine their efforts and imprison the Sharpteeth by tearing down the rock tower. The children cheer as the sharpteeth have been defeated and have a tooth for Saurus Rock.
Littlefoot and his friends then complete Littlefoot's self-assigned mission. Doc departs, remarking as he goes that Littlefoot already has a hero on whom to depend, referring to Littlefoot's grandfather, as Littlefoot glances back at his grandfather carrying his friends to the neck of Saurus Rock. He then glances back at Doc, who was already almost out of sight, as Littlefoot sheds tears, but runs back to his grandfather. He asked his grandfather how the new tooth looked, and his grandfather replied positively and Littlefoot wondered if the bad luck would finally be over. But his grandfather was starting to remind him, but Littlefoot finished it for him that there was no such thing as bad luck, but that there was no harm in making sure. Littlefoot and Cera later build a legend of their own based on this new paradigm, portraying Grandpa Longneck as a savor.
- Twilight Sparkle, Applejack, Rarity, Rainbow Dash, Pinkie Pie, Fluttershy, Spike (MLP), Sunset Shimmer, The Cutie Mark Crusaders (Apple Bloom, Sweetie Belle and Scootaloo), Thomas the Tank Engine, and Percy guest stars in this film.
- Sunset Shimmer will join Tino and his team in the end of this film.
- 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
- Kenneth Mars as Grandpa Longneck and the narrator.
- Thomas Dekker as Littlefoot
- Anndi McAfee as Cera
- Aria Curzon as Ducky
- Jeff Bennett as Petrie/Spike
- Kris Kristofferson as Doc
- Miriam Flynn as Grandma Longneck
- John Ingle as Cera's father
- Nancy Cartwright as Dana
- Sandy Fox as Dinah
- Danny Mann as Allosaurus