Littlefoot’s worries about the relationship between his old friends and his new friend Ali are soon replaced by a more urgent worry when Littlefoot’s grandfather is infected by a disease that the Old One, the leader of the migrating herd, diagnoses to be fatal unless the afflicted eats the healing petals of the Golden Nightflower, a plant that only grows in the Land of Mists. Worried by the tales of the changes in the outer world, Littlefoot’s grandfather takes a promise from Littlefoot; that Littlefoot leave the Great Valley with his grandmother and the herd in case of Grandpa's death, so as to remain safely with his cousins. The offer to join the migrants has already been made to them, though Littlefoot's grandparents had refused it.
As nobody is willing to risk a journey to the dangerous Land of Mists in order to obtain the Nightflower, Littlefoot decides to go himself and sneaks away at night. When he asks Ali to tell him the way to the Nightflower, she decides not to tell him the way, but lead him right to it. She only asks Littlefoot to go without his old friends Cera, Ducky, Petrie, and Spike, whom he had planned to ask for accompaniment. With mixed feelings, Littlefoot agrees.
The only way to reach the Land of Mists runs through a mysterious series of caves and caverns, in which Littlefoot accidentally sets off a rock slide. Neither child is hurt; but the fallen rocks cut them off from one another altogether. Ali therefore returns to the Great Valley as quickly as possible in order to get help from Littlefoot’s friends. When they learn about Littlefoot’s peril, Ducky, Petrie, and especially Spike overcome their antipathy against Ali. Cera, still too proud to trust Ali and offended by the fact that Littlefoot did not ask them to accompany him on the quest, decides to stay behind and sulk; a decision to which she does not adhere for very long.
Inside the cave, Littlefoot is unaware of what is happening beyond the debris lying between himself and Ali. Desperately he errs through the darkness of the cave, seeking another aparture. He there meets Archie, an Archelon, who initially tries to be scary, but fails altogether in his attempt to conceal his good nature. Archie tries to help Littlefoot dig through the debris of the rock slide; this proves considerably difficult even with Ali, Spike, Ducky, and Petrie's help from the other side. The situation becomes dangerous when Littlefoot and Archie encounter two other inhabitants of the cave; Ichy, an annoying Ichthyornis, and Dil, a nearly blind Deinosuchus, who remain together despite their mutual dislike because each of them is dependent on the other one. Ichy is too small and too weak to be able to hunt down sufficient prey, while due to her near-blindness Dil’s enormous size and strength would be useless without Ichy's guidance. Just when there seems to be no way for Littlefoot and Archie to escape the predators, Cera appears and with her hard head breaks through the debris of the rock slide, which temporarily renders Ichy and Dil insensate.
Cera’s opinion about Ali remains unchanged, even though the others have accepted her. Being rebuffed because she is a "Threehorn" has hurt Cera's nationalistic pride. When Archie for the first time learns of the reason for which Littlefoot and the others were in the cave, he shows them a shortcut through the caves to the Land of Mists.
Despite Ali’s warnings of the dangerous mists, Cera is soon separated from the others. Seeking for her, Littlefoot and the others encounter a great variety of creatures, most of whom appear unfriendly. An exception is a little ratlike creature (possibly an Alphadon or a Purgatorius) whom Ducky names Tickles, who helps the protagonists find Cera.
In order not to get further lost, Cera stays at the position where she had been when she had lost sight of her friends; when the mist thins, this proves dangerous. Unaware that she is at the edge of a river bank, Cera jumps up upon seeing her friends again, whereupon the edge on which she is standing crumbles into the rapid river and carries Cera along. While her friends are trying to rescue Cera from drowning in the river, Ichy and Dil appear. For them, Cera in the river seems to be an easy prey; however, a brave and perilous action of Ali's saves Cera and results in Cera's acceptance of Ali as a friend. Matters are further clarified when Ali explains her lifelong isolation and agrees musically that it "takes all sorts to make a world".
When night falls, the group has still not succeeded in finding the Nightflower. They therefore take a rest in a field of inconspicuous, closed blossoms. As they sleep, the full moon is revealed from behind the clouds. The wind bends the stems of the field, making the flowers appear to bow in reverence to the moon. Spontaneously they open, exposing themselves as Nightflowers. Spike and Tickles, being the first to see this, waken Ducky, who stirs everyone from sleep.
Returning home loaded with Nightflowers, the group again is attacked by Ichy and Dil, who have been following them. The protagonists run for their lives, taking refuge behind a stone. Ichy is not deceived; he finds Petrie and captures him, only to fight with Dil over whose prey Petrie is. Taking advantage of this argument, Tickles snatches Petrie and stuffs Dil's tail into Ichy's beak. Cera cannot resist gloating at her friend's strategem; unfortunately for her, this alerts the predators to her position.
In the resulting chase, the hunted and hunters must cross a river. One of the Nightflower blossoms falls, whereupon Ducky tries to retrieve it. Consequently she falls into enemy clutches and is soon the unconscious prize over which all are fighting. She is nearly pulled in half by Ichy and Petrie, then falls from the air onto Dil's snout. Dil immediately flips her into the air and waits with open mouth below. As the unconscious Ducky falls, Spike speaks for the first time since he was hatched, shrieking his foster-sister's name with all the vigour he can muster. Ducky is shocked into consciousness and catches a dry branch from which she hangs nearly safe, but remains inaccessible to her friends. Seeing the latter fact clearly, Ichy attempts to frighten them by sneering sadistically; but Spike appears to have had quite enough nonsense. Every inch the offended brother, he smites Ichy with his versatile tail, knocking the nasty bird into Dil's still-open mouth. Dil closes it, thinking she has caught Ducky. At that moment, Ducky and the others are on their way home, amazed yet at Spike's newfound ability to talk.
Below, in the river, Ichy exhorts Dil not to swallow him and to let him out. When Dil protests that she did not see Ichy, he rubs her nose in the fact, calling her useless. Furious, and narrow-minded in their fury, the two part ways, whereupon Dil is chased by a Plesiosaur (her fate is unknown).
Littlefoot and the others return to the Valley in time to save Littlefoot’s grandfather with the Nightflower, which also ensures that Littlefoot is to stay in the Great Valley. Soon after, Ali moves out with her herd; according to the epilogue, Littlefoot and the others will meet her again. This promise is fulfilled in the television series, though none of the film's sequels mention Ali; thus fulfilling the narrator's description of the meeting as "another story", in that it occurs in a different timeline featuring the same characters.
Note: The Japanese voice actors are appearing so far.