A curious fairy girl named Crysta sees a part of the world she has never seen before beyond FernGully, a rainforest near Mount Warning, Australia. She believes humans dwell on Mount Warning, but the wise sprite of the forest and Crysta's motherly figure, Magi, says humans are now extinct, driven away by Hexxus, the spirit of destruction and all that is toxic to nature, never to return and presumed dead; Hexxus was defeated by the fairies and imprisoned inside a tree. Crysta mentions a black cloud that she saw rising near the mountain, and Magi identifies it as smoke, but dismisses her speculation that the smoke might be Hexxus.
Befriending an uncoordinated and comical fruit bat named Batty Koda who has been experimented on by humans and now has wires and antennae fused into his head, Crysta heads to Mount Warning where she finds dead trees all marked with red aerosol paint crosses, which mark them for cutting. The source of the smoke is the exhaust from a huge tree leveler. She finds male humans, and accidentally shrinks one named Zak in trying to prevent him from being crushed by a tree. Batty swoops in and rescues Zak and Crysta caught in a spider web on that tree.
Zak goes on a wild adventure with Crysta and Batty, dodging a hungry Goanna lizard named Lou, and begins to fall in love with Crysta. Meanwhile, Zak's superiors, Tony and Ralph, cut down an enchanted baobab tree that Zak had inadvertently painted an X mark on as he tried to spray a fly bothering him, discovering too late that Hexxus has been released from the tree. Seeking revenge upon the fairies of FernGully for imprisoning him, Hexxus gains power by feeding on the pollution, specifically the energy and smoke produced by the leveler. He manipulates the lumberjacks and their tree leveler into tearing down the rainforest in the direction of the fairies by the next morning.
Eventually, Zak tells the truth about who he is and how the humans are destroying FernGully. The fairies join forces and fuse their powers together, creating a protective tree cage. Magi sacrifices herself, giving her power to the fairies and Zak, leaving Crysta and the other fairies to defeat Hexxus. Zak turns off the leveler, making Hexxus lose all the energy he was gaining from it and disappear, but he soon rips out of the machine as a giant fire-breathing skeleton creature made of oil. Crysta seemingly sacrifices herself like Magi did by allowing Hexxus to devour her completely, and uses her powers from inside him to grow a seed she had with her, imprisoning both Hexxus and the leveler inside a new tree with help from the fairies led by Pips, (a friend of Crysta's who is both romantically interested in her and jealous of her relationship with Zak). Soon afterwards, she emerges, unharmed and alive, from a flower. Crysta sadly resizes Zak to normal size and he sets off with his fellow lumberjacks to try to stop the destruction of the rainforests. Crysta takes Magi's place after finally learning how to control her powers.
- Littlefoot, Cera, Ducky, Petrie, Spike, Chomper, Ruby, Guido, Grandpa Longneck, Grandma Longneck, SpongeBob SquarePants, Patrick Star, Squidward Tentacles, Sandy Cheeks, Mr. Krabs, Simba, Nala, Timon, Pumbaa, Taran, Princess Eilonwy, Fflewddur Fflam, Gurgi, Genie, Kronk, the Mighty Morphin Power Rangers, Zhane, Korra, Mako (Legend of Korra), Bolin, Asami Sato, The DigiDestined and their Digimon, Woody Woodpecker, The Crime Empire (Joker, Harley Quinn, Two-Face, The Penguin, Negaduck, Megavolt, Quackerjack, Bushroot, and The Liquidator), Dr. Facilier, Sheldon J. Plankton, The Horned King, Creeper, The Grand Duke of Owls, and Team Rocket (Jessie, James and Meowth) guest star in this film.
- The Crime Empire, Dr. Facilier, Plankton, The Horned King, Creeper, The Grand Duke of Owls, and Team Rocket will work for Hexxus in this film.
- Before the events of this film, Bowser (who already guest starred in Winnie the Pooh Goes to FernGully: The Last Rainforest) puts The Horned King in charge of the mission to free Hexxus.
- In this film, Littlefoot, SpongeBob, Taran, and their friends will meet Batty Koda for the first time.
- This is the first Pokémon crossover to guest star The Crime Empire and The Digidestined and their Digimon. It is also the first Pokémon crossover to guest star characters from SpongeBob SquarePants, The Black Cauldron, and Mighty Morphin Power Rangers.
- This is the first non-Disney crossover to guest star Littlefoot and his friends.
- Mighty Morphin Power Rangers: The Movie, Turbo: A Power Rangers Movie, Digimon: The Movie, and FernGully: The Last Rainforest were all released by 20th Century Fox.
- Aladdin, Rock-a-Doodle, and FernGully: The Last Rainforest were all released in theaters in 1992.
- The Land Before Time IX: Journey to Big Water was first released directly on VHS and DVD in 2002, the same year The Land Before Time II: The Great Valley Adventure, The Land Before Time III: The Time of the Great Giving, and FernGully: The Last Rainforest were first released on DVD, Pokémon 4Ever was released in US theaters, and The Lion King was re-released in IMAX theaters.
- The Land Before Time XI: Invasion of the Tinysauruses was first released directly on VHS and DVD in 2005, the same year The SpongeBob SquarePants Movie was first released on VHS and DVD and both Rock-a-Doodle and FernGully: The Last Rainforest were re-released on DVD.
- The Lion King 1½, The Lion King II: Simba's Pride, and FernGully: The Last Rainforest were first released on Blu-ray in 2012.
- Ash, Littlefoot, SpongeBob, Simba, Tai, and their friends will face Hexxus again in Pooh's Adventures of The Elm-Chanted Forest.
- Like BowserMovies1989's film, Winnie the Pooh Goes to FernGully: The Last Rainforest, this is an NTSC film with NTSC bits from the Pokémon films, The Land Before Time films, The SpongeBob SquarePants Movie, The SpongeBob Movie: Sponge Out of Water, The Lion King films, The Black Cauldron, the Aladdin films, The Emperor's New Groove, Kronk's New Groove, Digimon: The Movie, Batman: Mask of the Phantasm, The Princess and the Frog, and Rock-a-Doodle.
- Tail and his friends first met Batty Koda in Pooh's Adventures of The Pagemaster.
- Ash, Simba, and his friends first met Batty Koda in Pooh's Adventures of The Santa Clause.
- Ash, Littlefoot, SpongeBob, Simba, and their friends will see Batty Koda again in Winnie the Pooh and SpongeBob SquarePants Go to Jurassic Park.
- Both Genie and Batty Koda were voiced by the late Robin Williams.
- The film will be dedicated in memory of Robin Williams (who voiced Batty Koda in the real film and Genie in Aladdin) who committed suicide on August 11, 2014 and John Hurt (who voiced The Horned King in The Black Cauldron) who died for an unknown reason on January 27, 2017.
- Yru17 originally planned to re-edit separate Land Before Time and SpongeBob SquarePants crossovers with the two FernGully films (with Simba, Taran, and their friends guest starring and Dr. Facilier working for Hexxus in the SpongeBob versions and Genie guest starring in The Land Before Time versions), but he retired from making anymore crossovers, so Daniel Esposito will guest star Littlefoot, SpongeBob, Simba, Taran, and their friends in the two Pokémon/FernGully films instead, considering that a crossover with the first film should mark the first time Littlefoot and his friends would meet Batty Koda and face Hexxus.
- Ironically, Crysta's father (Ash) has the same first name as the main protagonist from Pokémon, who is Ash Ketchum.
- This film actually takes place after Littlefoot's Search for The Black Cauldron (which explains Ash Ketchum, Littlefoot, and their friends and Genie already knowing Taran, Princess Eilonwy, Fflewddur Fflam, and Gurgi and facing The Horned King and Creeper) and SpongeBob and Friends Find The Black Cauldron (which explains SpongeBob, Simba, and their friends already knowing Taran, Princess Eilonwy, Fflewddur Fflam, and Gurgi and facing The Horned King and Creeper).
- This is Daniel Esposito's second non-Disney crossover after Ash's Adventures of Space Jam.