As the opening song of the film (Peaceful Valley) indicates, Littlefoot and company's arrival to the Great Valley is a relatively recent occurrence. The children are living happily in their new home, under their families' watchful eyes. They also reunite with Tino Tonitini, Lor McQuarrie, Carver René Descartes and Tish Katsufrakis and meet their friends Doraemon, Noby, Sue, Sneech, Big G, Twilight Sparkle, Applejack, Rarity, Rainbow Dash, Pinkie Pie, Fluttershy, Spike, The Cutie Mark Crusaders (Apple Bloom, Sweetie Belle and Scootaloo), Thomas, and Percy. When the gang tries to get to the sheltering grass to play, but land in the tar pit surrounding it, the grownups come and save them and chastise them for disobeying them, then lecture them that night. Cera then tells the others that they need to prove they are independent by running away for a while into the Mysterious Beyond, a location just outside the valley. Before they leave, they notice two egg nappers, Diamond Tiara, Silver Spoon, and Diesel 10 stealing an egg from Ducky's nest. They chase them into the Beyond, during which a landslide occurs. The egg rolls safely back to the nest, but the five are under the impression that it was destroyed in the landslide. This upsets Ducky until she notices what looks like the egg, only slightly larger.
The gang "return" this egg to the Valley, only to find out that the stolen egg and this one are not the same. They decide to hatch it, nonetheless, until the egg hatches, revealing a baby sharptooth. While the others run away, Littlefoot decides he's safe, and tries to raise the hatchling on leaves, to no avail. When he hears the others calling for help, as the egg nappers Ozzy and Strut, Diamond Tiara, Silver Spoon, and Diesel 10 are attacking them, he runs to their aid, while "Chomper" follows him. Chomper's shadow frightens the villains away, after which Littlefoot exchanges introductions between Chomper and the others. They accept him, until he bites Cera by instinct. He is told this is considered bad behaviour in the Great Valley, and runs off. When the others follow him, they find him chasing insects on top of the Smoking Mountain (volcano).
Ozzy and Strut, Diamond Tiara, Silver Spoon, and Diesel 10 attack the children and the others again, but Chomper once more comes to the rescue, biting onto Strut's tail. At that moment, the volcano erupts, slowly oozing lava in the children's path. Littlefoot pushes a tree over a canyon, to make a bridge for the others. Once across, they find two adult Sharpteeth on the other side. They escape them, and make it back to their families. After fighting the Sharpteeth off, the adults inquire how they entered the valley, to which the children confess over their adventure the night before, and the landslide which resulted. The adults set off to block the new entrance to the valley, and tell the children to stay behind. Littlefoot runs off to find Chomper, but is chased by one of the Sharpteeth. When trapped in a rotting log, they are approached by the sharpteeth. Then, Chomper calls to them, and they recognize him as their son. They then leave with him. Littlefoot, while out of the log, gets captured by Strut and Ozzy. Chomper hears Littlefoot screaming, and he goes to save him. Then Chomper's parents chase the egg nappers into the Mysterious Beyond again, the villains have retreated, and Littlefoot and Chomper say their final goodbyes. Littlefoot returns to the other plant-eaters. Littlefoot's grandpa tells him from then on, he should stay close to the herd. Then, he helps in knocking down some more rocks to seal up the entrance between the Great Valley and the Mysterious Beyond.
- Twilight Sparkle, Applejack, Rarity, Rainbow Dash, Pinkie Pie, Fluttershy, Spike the Dragon, The Cutie Mark Crusaders (Apple Bloom, Sweetie Bell and Scootaloo), Thomas, Percy, Diamond Tiara, Silver Spoon, and Diesel 10 guest stars in this film.
- Diamond Tiara, Silver Spoon, and Diesel 10 will work for Ozzy and Strut.
- Even though Twilight, Thomas and their friends already meet in Littlefoot and his friends Pooh's Adventures of Thomas & Friends: Misty Island Rescue, Twilight will use a time traveling spell, making her and her friends to back in time right before they meet Ruby and Chomper.
- This film will be dedicated to the loving memories of Kenneth Mars (1935-2011), who was the then-current voice of Grandpa Longneck and died of pancreatic cancer, Linda Gary (1944-1995), who was the original voice of Grandma Longneck and died of brain cancer, and John Ingle (1928-2012), who was the film's narrator and the then-current voice of Topsy (aka Cera's father) and died of cancer.
- 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
- 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
- Scott McAfee as Littlefoot
- Candace Hutson as Cera
- Heather Hogan as Ducky
- Jeff Bennett as Petrie / Ozzy
- Rob Paulsen as Spike / Strut / Chomper
- Kenneth Mars as Grandpa Longneck
- Linda Gary as Grandma Longneck
- Tress MacNeille as Petrie's Mother / Ducky's Mother / Maiasaura
- John Ingle as Narrator / Cera's father
- Chantal Strand as Diamond Tiara
- Shannon Chan-Kent as Silver Spoon
- Matt Wilkinson as Diesel 10