Littlefoot, a young Apatosaurus living in the verdant Great Valley, is eagerly awaiting the arrival of his father Bron, who returns to the valley with his herd once a year. However, he soon learns from a Nothronychus member of his dad's troupe named Wild Arms that his father became stranded in the wilderness when the "fire mountain" erupted, leaving the rest of the herd to go on without him. Embarking on a journey with his friends - Cera, Ducky, Petrie, and Spike - Littlefoot enters the Mysterious Beyond to try and rescue him on their own.
After an encounter with a duo of "featherhead sharpteeth", and a disagreement between Littlefoot and Cera on which path to take, Littlefoot decides to go ahead alone, where he meets a Pteranodon named Etta who knows his father. When the two become trapped in a cave, she sings a song to lead him on his way, and he is eventually reunited with his friends as they continue their journey together with Etta into the harsh landscape. Meanwhile, the elder dinosaurs learn about their children's trek, and decide to go after them with two younger ones - Chomper and Ruby. They attempt to have Wild Arms guide them back to where Bron was last seen, but he faints at the mere sight of Chomper, a "sharptooth", and has to be carried, leaving Chomper to lead the way with his nose.
Etta eventually leads Littlefoot and his friends to the fire mountain where they find Bron. They learn that he became trapped and separated from his herd when he went back to save Wild Arms, who was in danger due to his cowardly nature. Reunited with his father and the rest of the herd led by Chomper, the group extol the virtues of working together and finding bravery through companionship.
- Doraemon, Noby, Sue, Sneech, Big G, Twilight Sparkle, Applejack, Rarity, Rainbow Dash, Pinkie Pie, Fluttershy, Spike (MLP), Annoying Orange, Pear, Passion Fruit, Midget Apple, Marshmallow, Grapefruit, Grandpa Lemon, Nerville, Princess Sapphire, Choppy, Prince Frank, Discord, Sunset Shimmer, The Human Mane 5, Sci-Twi, Spike the Dog, The Cutie Mark Crusaders (Apple Bloom, Sweetie Belle and Scootaloo), Thomas the Tank Engine, and Percy guest stars in this film.