Crysta is taking care of three baby animals and demonstrating greater control over nature. She and Pips begin a small contest over who can grow the more impressive plant, while Pips expresses a desire to see more of the.
Suddenly, Batty Koda arrives in a panic, warning that human poachers are right behind him. These poachers show up with their dogs and capture the three baby animals. The first rescue attempt while still in Ferngully fails, and results in a huge forest fire, destroying a huge part of the forest and scarring Mother Kangaroo. Pips and the Beetle Boys volunteer to follow the humans to town and rescue the babies, convincing the reluctant Batty to be their guide. They arrive at a town. They are so fascinated by the rides, they are reminded by Batty to resume their mission.
All this time the fairies have been healing the rainforest and Crysta finds and helps one of the poachers' dogs (she called him Boof) abandoned and caught in a trap. She takes him on a journey to the town. Pips and the Beetle Boys meet a girl named Budgie who is hard at practicing for the clown act. Pips flies over to her and introduces himself and his friends. She gives them shelter in her trailer. Batty has located the poachers' place but the others ignore him too fascinated by modern human utilities. Bark and Batty go to make a rescue attempt, but Batty is caught.
Budgie tells Pips that she has been working on her clown act for years, but she has never been all that good. Pips tells her that she is trying too hard, and she should just do it. Back at where the babies are, the animals are very scared and fear they will never get. Batty overcomes his terror of the situation and manages to reassure them. Then the poachers take all the cages and load them onto a big truck. At the fair, Budgie goes to a contest stand and wins a stuffed kangaroo, which reminds Pips of the babies he's supposed to be saving. He tells Budgie about them and she offers to help him out.
They all reach the old warehouse. The poachers drive off, and Budgie jumps off a ledge and lands on the truck. They drive past Budgie's grandfather, and he sees that Budgie is hanging on the, and he drives after them. Budgie manages to get inside the car and frees all the birds in the cages. The poachers see Budgie trying to get in the car and are enraged seeing all the birds flying away. One of them climbs out of the truck and tries to get Budgie off. She manages to get away from him, but he unlatches the car she's on and sends her rolling backwards on the road. She ends up with one side of the car dangling off a cliff. Batty and Budgie's grandfather manage to save her.
The group then head by clown car to the ship where the animals are being loaded. Pips undoes the conveyor catch so that the catches land in Budgie's grandfather's car. A struggle for the cages ensues between the poachers and Budgie. Boof and Crysta arrive to help. The other dog turns against his former master. The boat gets away and the fairies use their magic to stop it growing a gigantic tree. Nugget almost drowns as he escapes. Budgie and her grandfather adopt Slasher and Boof while all the animals and fairies return home.
- Emerl/Chaos Emerl
- Donkey Kong & Diddy Kong
- Twilight, Rainbow Dash, Pinkie Pie, Rarity, Applejack, Fluttershy & Spike
- Applebloom, Sweetie Belle & Scootaloo
- Shining Armor & Princess Cadence
- Spongebob, Patrick & Sandy
- Skipper, Kowalski, Private & Rico
- Finn & Jake
- Eddy, Double-D & Ed
- Rigby & Mordecai
- Gumball & Darwin
- Blossom, Bubbles & Buttercup
- Sam & Max
- Sora, Donald & Goofy
- Huey, Dewie & Louie
- Rich, Dave, Smitty & Scott
- Ralph, Felix & Vanellope
- Thomas, Luke, Hiro, Charlie, Paxton, Victor, Kevin, Duck, The Logging Locos & The Steam Team (Percy, James, Gordon, Henry, Edward, Toby and Emily)
- Xion (Cameo)
- Darkrai & Meloetta
- Mrs. K
- Mr. Chuckles
- Boof & Slasher
- The sequel takes place at Thomas and Twilight Sparkle Goes to FernGully: The Last Rainforest