Every year, as the warm season approaches, a certain tree in the Great Valley blooms with pink flowers. Because of the tastiness of these "treesweets", every dinosaur in the valley wants his/her fair share of it. However, because of this tastiness (and the fact that there seems to be only one such tree in the whole valley), there is hardly enough for everyone. Because of this, none may eat any of the treesweets until the day they "reach the peak of their tastiness".
As the film begins, Tino, Doraemon, Thomas, Twilight Sparkle, their friends, Littlefoot and his friends Ducky, Petrie and Spike are eagerly waiting to nibble the first treesweets. Ducky is about to take one, but Littlefoot quickly tells her to stop and reminds them all that none may take any treesweets until "Nibbling Day". This however, doesn't stop Petrie from flying to the tree's crown and trying to take one. Just then, Cera's father emerges and states very clearly how every dinosaur in the valley has waited a long time to taste the treesweets. As Cera, too, appears before them, she reminds them that she is the one who is supposed to get the first treesweet because she was the one who found the treesweet-tree in the first place, although it was indeed Littlefoot who did it. Cera also teases Littlefoot for being too little to actually reach the treesweets.
Meanwhile, Cera's father is visited by an old friend—a female treehorn named Tria -- whom, it seems, he used to have a crush on. She also reveals his name to be Topsy (although it may simply be a nickname). After speaking a while with her, he promises Tria that she will get the first treesweet of the season; which Cera, who appears just in time to hear him say this, becomes very upset about. From that moment on, Cera refuses to make friend with Tria and simply shrugs her off whenever she tries to talk to her.
Littlefoot, meanwhile, goes off by himself, feeling very down about how "little" he is. As he returns to the treesweet tree, he climbs up the cliff right next to it and tries to reach the treesweets by himself. As he does, he accidentally falls right through the tree and knocks down every single treesweet. Realizing the trouble he is now in, he faints. As he wakes up, he finds himself surrounded by several miniature longnecks. They have eaten all the treesweets and quickly run away once the shocked Littlefoot starts screaming out of fear.
Upon noticing that every treesweet is gone, all the dinosaurs in the valley are standing in front of the tree; many of them, including Topsy, suspecting Littlefoot to be the guilty party. Littlefoot, afraid to admit it was his fault that the treesweets fell off the tree, blames everything on the tiny longnecks. At first, no one believes him, but when they see evidence of tiny teeth marks on a tree sweet, he is believed and everyone starts looking for the tiny longnecks, preparing to drive them out of the valley once they have been found. As Littlefoot and Cera are searching the valley, Littlefoot falls down a pothole in the ground where, it turns out, the tiny longnecks are hiding in. First being afraid of them, Littlefoot flees deeper into the cave; but soon enough, he finds out that the tiny longnecks are not as bad as he thought and befriends them. Upon hearing how difficult it is for the tinysauruses to find food, he promises to help bring them as many treestars as he can every night.
Eventually, Littlefoot feels ready to tell his friends about the colony of tiny longnecks living in the underground caverns. They all get to see the tiny longnecks for themselves, and promises not to tell the adults. Even Cera, who is still angry with her father, promises to keep it secret, mainly because she finds out that she can relate more to them than she would've imagined. Many of the tinysauruses in the colony feel that their leader, Big Daddy, bosses them around a bit too much, though he simply wants their best. As to the reason that he doesn't trust the "bigger" dinosaurs is that they, in his opinion, only seem to think: "Because they're bigger, it makes them more important".
When sneaking off to see the tinysauruses again, Littlefoot and his friends are busted by Topsy. But when he tries to ask them why they are out so late at night, Cera angrily throws the question back at him. Topsy, not wanting Cera to find out about him and Tria, manages to see them off. Just as Tria comes up to him, they spot one of the tiny longnecks. A chase ensues which eventually reveals their hideout. As the grown-ups prepare to block the caverns; Littlefoot, realizing that he must tell the truth, admits that it was his fault that the treesweets are gone, and not the tiny longnecks'. However, just as he's finished, the tinysauruses' cavern collapses, trapping the tinysauruses inside. The tinysauruses escape. The tinysauruses run into two Sharpteeth Utahraptors that chase them and find their way into The Great Valley. Meanwhile, Littlefoot's friends are mad at him. They later try to apologize to him for being angry. However, they mistake the Sharpteeth for Littlefoot. The two carnivores lunge at them, causing a chase. Littlefoot shows up just at the right time and saves Ducky just as she was about to get eaten. When all seems lost, the tinysauruses show up and fight the Sharpteeth. The grown-ups of the Great Valley then show up and drive the sharpteeth back into The Mysterious Beyond through a hole. Then they cover up the hole with a large boulder. Nibbling Day finally comes at last. Everyone eats, parties, and acts merry. The film ends with Petrie clutching a treesweet.