Littlefoot notices a longneck herd entering Great Valley, and informs his grandparents. They tell him that the longnecks are thier far away friends, and that they must go and greet them. As the Old One, the leader of the herd, tells the residents of the great valley that her herd has been migratory since a heavy rain period turned their old home into a marshland called "The Land of Mists", and became the home of many dangerous creatures, Littlefoot meets a longneck girl named Ali, and invites her to play. He introduces her to his friends and Pooh and the others, but as she is not used to associating with diverse species, she is afraid of them.
Meanwhile, Grandpa falls ill, and the Old One notes that the illness is lethal unless the victim eats the petals of the "Night Flower", a flower which can only be found in the Land of Mists. Though Littlefoot is warned that the journey is too dangerous, he feels determined to save his grandfather, and asks Ali to take him there. She agrees, on the condition that the other children do not come; they will slow them down. As the two of them make their way, they pass through a cave, and sudden earthshake (earthquake) causes a wall of rocks to crash down, separating them. Ali decides the others will have to help her free Littlefoot, and runs off to get them. Littlefoot, in the meantime, tries to find a way out, and meets an old Archelon named Archie, who offers to help him dig through the rocks. They are interrupted by a belly dragger and a sharp beak named Dil and Ichy, (whom Jessie, James, and Meowth of Team Rocket are working for) who have their minds set to eat them.
While Ichy and Dil give Archie and Littlefoot chase, Ali and the others dig at the wall from the other side. After Cera (who initially refused to join out of spite for Ali) joins them, they are able to free Littlefoot and Archie, and knock Ichy and Dil out. Littlefoot explains to them what happened, and the night flower is mentioned. Archie shows them a way to the Land of Mists, and gives them a reminder to stay close together, for defense. In the Land of Mists, Cera becomes separated from the group, who seek help from a mammal Ducky names "Tickles" (for his fur) to find her. Cera falls into a river, and is soon pursued by Ichy and Dil. Ali saves Cera and distracts the predators, after which Cera softens towards Ali, and Ali explains her prejudiced behaviour.
When the 18 stop for the night, they find that they are in a field of Night Flowers, and quickly stock up on them. As they make their way home, Dil and Ichy attack them one more time. During the chase, Ducky falls into a river and Spike calls out her name, while Petrie rescues her from the predators. Ichy and Dil get into an argument when Dil mistakes Ichy for Ducky and eats him, after which they dismiss each other. Dil flings Ichy off, but soon calls for him when a Elasmosaurus gives her chase. Meanwhile, the children say goodbye to Tickles, and head home. They give Grandpa Longneck the blossoms, and he gets better upon eating them. Ali's herd then leaves, and the narrator concludes that Littlefoot and the others will meet Ali again one day, which has only happened in one episode of the TV series. She has yet to appear in another film.
- Ash Ketchum, Ttark, Kids World's Adventures Team, and Team Rocket (Jessie, James, and Meowth) guest star in this film.