The beginning of the episode shows Crysta 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, meanwhile revealing that Pips wishes to see more of the outside world.
Sonic, Tails and Crysta on the X Tornado heads to Mount Warning in the search for another Chaos Emerald where they finds dead trees all marked with red aerosol paint crosses, which mark them for cutting. The camera then pans through the trees to reveal the source of the smoke, which turns out to be the exhaust from a huge tree leveler. Crysta finds male humans, and accidentally shrinks one named Zak in trying to prevent him from being crushed by a tree. He gets stuck on a spiderweb on the tree that's just about to go through a tree shredder. She tries to get him off but can't when Batty swoops in, grabs them both off of the spider web and blames Crysta for her almost getting killed, because she did not listen to him. But Eggman arrives and the Egg Cerberus charges at Sonic and Tails, and misses, but Tails drops the Emeralds, and Eggman steals them! Tails throws a Power Ring in Sonic's hand, and Sonic defeats the Egg Cerberus and gets the Emeralds back.
Sonic and Tails chase the Egg Carrier on the Tornado-1 and take out the turrets, causing Eggman's battleship to escape. Sonic and Tails decide to return to FernGully.
Zak goes on a wild adventure with Crysta and Batty, nearly getting eaten by a hungry Goanna lizard named Lou, and unexpectedly falls in love with Crysta. Meanwhile, Zak's superiors cut down an enchanted baobab tree that Zak had inadvertently painted an X mark on while trying to spray a fly that was buzzing around him. Unfortunately, this turns out to be the tree Hexxus is trapped in, and the cutting down and processing of the tree by the lumbermill-like leveler machine releases him. Determined to get revenge upon the fairies of FernGully (specifically Magi Lune) for imprisoning him, Hexxus apparently gains power from the pollution, specifically the energy and smoke produced by the Leveler, as he can be seen "drinking" from it like a liquid. He manipulates the lumberjacks and their tree leveler into tearing down the rainforest in the direction of the fairies by the next week, thereby destroying the very fabric of their world. He does this under the vocal guise of their boss.
Shortly after, Batty arrives in a panic, announcing that two human poachers are right behind him. These poachers show up with their dogs and promptly capture the three baby animals. The first rescue attempt while still in FernGully fails, and sadly results in a huge forest fire, destroying a huge part of the forest and injuring the mother of the captured baby kangaroo Nugget. Pips and the Beetle Boys volunteer to follow the humans to town and rescue the babies, convincing the extremely reluctant Batty to be their guide.
- In the movie, Hexxus, acting as the boss, tells Tony and Ralph to tear down the rainforest in the direction of the fairies by the next morning. In this episode, he tells them to destroy the fairies' world by the next week.
- The Red paint job of the original Tornado and its outside construction, the ability to transform into an X-shape like the Tornado 2, and the homing missiles found on the Tornado 3.
- When Tails transforms the plane there is writing near the rear of the plane that reads "Tornado 03".
- The huge forest fires destroy a huge part of the forest before Hexxus reaches FernGully with the leveler. The fairies restore the forest.