After eight tadpoles become toadlets, they find themselves alone in a strange and dangerous forest. Immediately threatened by a hungry snake named Erebus, Beauty Stem says that they must all stay together and Fur Foot tries to lead them. However, Elf Cup and Shaggy Mane want to go off and play, while Panther Cap finds himself drawn away from the others by voices that only he can hear. Fur Foot, Beauty Stem, Puff Ball, Oyster, Slippery Jack and Panther Cap soon begin a journey together. They immediately face danger in the form of rushing rapids and then when Panther Cap goes off to follow the voices, Beauty Stem decides to accompany him. Meanwhile, Elf Cup and Shaggy Mane find themselves in danger from a ""wind rider,"" not even knowing that the others are headed their way to try to bring them back into the fold. Eventually, all are reunited and meet up with a wise toad named Mistle Toad, who warns them that they have missed the great migration. They must all head immediately for the Fair

Shaggy Mane's antics slow the Toad Patrol as he disturbs a nest of wasps, gets caught in the headlights of an oncoming 'Rumble Crusher', and loses a close encounter with Cleopatra the Skunk. Feeling useless, he runs away, until Cleopatra and Earth Star, a wandering Toadlet minstrel, convinces him that he is a vital member of the Toad Patrol.

On the way to a Thunder Tree, a friendly 'Tunnel Toad' guides the Toad Patrol through a Toad Tunnel under the highway where they wait in helpless suspense for Fur Foot, Puff Ball and Elf Cup who are trapped in a fire that threatens their new friend, Morton the Turtle.

Earth Star helps the Toad Patrol find shelter but mysterious Crystals turn the Toadlets against each other as a flood threatens to seal them into a crystal cavern built by the Ancients.

Oyster and Slippery Jack are scooped into a bucket by a 'little stomper' and escape from a camper with the help of two vaudevillian mice, Rosencrants and Guildenstern.

Beauty Stem and Panther Cap come face to face with their innermost fears when crossing an eerie toadstool graveyard to find Earth Star and save Mistle Toad, who is trapped on the ledge of a steep cliff.

The Toad Patrol faces the dangers of a forest night when they discover the Elf Cup has run off to meet EarthStar. At first, only Mistle Toad believes her story that she saw the Ancients wandering through the moonlit woods.

Digger, a mole who looks out for number one, over hears the Patrol's Plans and tells Erebus. Erebus traps Panther Cap amd waits for the other Toadlets to come and rescue him.

The Toad Patrol are trapped in a bird house when a woodpecker steals Panther Cap's acorn. With the help of a sleepy porcupine, they circumvent a couple of boisterous flying squirrels and plead for the return of the precious acorn that points them to the great Thunder Tree.

Beauty Stem falls ill when she drinks polluted water. Mistle Toad, EarthStar and the Toad Patrol trek through the night to reach an Ancient healer in time to save Beauty Stem's life.

While exploring an abandoned temple of the Ancients, Mistle Toad and the Toad Patrol are trapped by Belisarius, the leader of a bat pack.

The thunder trees have guided the toadlets on the final path to the Fairy Ring and now all that's left is to enter it to reach Toad Hollow. They, however, find themselves facing obstacles both practical and villainous in the final race to make it before the yellow ball goes down and they all become toadstools. After rescuing Earth Star from Erebus and a muddy pit, the toadlets face a large rift between them and the final path to Toad Hollow. Badgered by both Medea and Erebus along the way, Panther Cap and Earth Star find themselves trapped in the cracks. There, they share some heart-to-hearts on why Earth Star wants to stay in the forest and what exactly happened between Earth Star and his friends. Meanwhile, the other toadlets face a desperate decision as to what to do to save their friends, while still making it to the Fairy Ring in time. Fortunately, Mistle Toad is also around to help out.