Jesse, the boy who freed Willy the orca two years ago and teamed up with Celebi to help Littlefoot and the gang help Taran, Princess Eilonwy, Fflewddur Fflam, and Gurgi find The Black Cauldron the following day, has been adopted by his foster parents, Glen and Annie Greenwood. It has also been a year since Jesse teamped up with Randolph to help Littlefoot and the gang helpCharlie Barkin and Itchy save Anne-Marie from Carface and find new parents for her one year later. Jesse, now a teenager, is reunited with Littlefoot, Cera,Ducky, Petrie, Spike, Chomper, Ruby, Guido, Hyp, Mutt, Nod, Ash Ketchum, Pikachu, Misty, Brock, Togepi, Celebi, Stan Marsh, Kyle Broflovski, Eric Cartman, Kenny McCormick, Mickey Mouse, Donald Duck, Goofy, Bugs Bunny, Daffy Duck, Genie, Zazu, Woody Woodpecker, Taran, Princess Eilonwy, Fflewddur Fflam, Gurgi, Doli, Mikey Walsh, Brand Walsh, Mouth Devereaux, Data Wang, Chunk Cohen, Andy Carmichael, Stef Steinbrenner, Sloth Fratelli, Scooby-Doo, Shaggy Rogers, Fred Jones, Daphne Blake, Velma Dinkley, Slimer, and Stay Puft, meets Littlefoot's grandparents, Cera's half-sister Tricia, Petrie's reformed uncle Pterano, Kyle's adopted brother Ike Broflovski, Littlefoot's other friends Esmeralda, Djali, Jack Skellington, The Jungle Book Vultures (Buzzie, Flaps, Dizzy, and Ziggy), and his newest friend Jiminy Cricket, has an eye for girls, and is preparing to go on a family camping trip to the Pacific Northwest. Before they leave town, however, Jesse's caseworker Dwight informs him that his birth mother, who abandoned him eight years before, has died in New York City. To add to his dismay, Jesse has to contend with the sudden presence of his overly talkative and mischievous younger half-brother, Elvis (Francis Capra), who is a virtual stranger to him and has his own dinosaur friends Rex, Elsa, Woog, Elsa, and Dweeb. Littlefoot asks Taran if he and the rest already knew Rex and the gang and Taran replies "It's a long story, Littlefoot". Elvis is prone to telling lies and easily gets on Jesse's nerves. They are invited on their long camping trip so that he and Jesse might get to know one another and the dinosaur relatives could spend some quality time with Littlefoot and the gang.
On this trip, Littlefoot tells Jesse what new friends he and the gang made friends with recently (for example, Fievel Mousekewitz from An American Tail, Danny and Sawyer from Cat's Don't Dance (even though they will guest star in the Pooh version), and The Good Fairies from Sleeping Beauty) and how they first met Jack Skellington, the Ghostbusters, and Aladdin. Eventually, Littlefoot and the rest are surprised to see the reformed witches (Orddu, Orgoch, and Orwen) again since they last saw them being King Gator's servants. Jack asks Littlefoot if he and the gang already know them and Littlefoot replies "It's a long story, Jack". Along the way, Jesse reunites with his old Native American friend Randolph Johnson (August Schellenberg), a Haida, along with Professor Oak, Ludwig Von Drake, Rafiki, Mr. Thicknose, and Dallben, and quickly becomes smitten by Randolph's goddaughter, Nadine (Mary Kate Schellhardt). As the youngsters grow closer, Jesse, Littlefoot, and the rest help Nadine befriend Willy, his whale siblings, Luna and Little Spot, and Littlefoot's old friend Mo.
As they continue to enjoy their camping trip, an oil tanker runs aground and spills oil into the ocean, trapping the three young whales in a small cove. When word gets out that the whales are trapped and Luna is dying from the oil in her lungs, the president of the oil company (Jon Tenney) arrives with a great plan to move the whales into captivity where they can recover from their injuries. His real plan, however, is to sell the whales to marine mammal parks and have them perform in shows. Oogie Boogie, Creeper, Ozzy, Strut, Ichy, Dil, Rinkus, Sierra, Red Claw, Screech, Thud, Pete,the Ancient Minister Asajj Ventress King Dedede Escargoon Star Wolf Team Dr Robotnik Scratch Grounder Coconuts The Nostalgia Critic The TGWTG Squad The Angry Video Game Nerd Benethlooney Darth Maul Savage Opress Malness and the Killers Kaptain Scuvry and his Crew Rocky Mugsy Dr Cortex and his Minions Ganon and his Minions the Mad Bunny and his Minions Wizardhiemer I.M.Meen Ophelia Chill Bowser Bowser jr Misstress Nine Azula the Pshyco Rangers the Phantom Blot Harry Marv the Trix Lord Darkar Valtor Dr Facilier Elmyra Duff Father the Delightful Children The Werecats Arthur Cecil Scar the Hyenas the Grand Duke of Owls Sodarn Insane King Ghidorah SpaceGodzilla Megalon Gigan Judge Doom the Toon Patrol the Leauge of Super Evil Invader Zim Gir Baron Greenback Valentine Queen La Doctor Doctor and her Minions Hacker Buzz Delete BurgerMesiter MesiterBurger Girmsly BurgerMesiter MesiterBurger's Minions Jafar Maleficent Myotismon Fat Tony Mr Burns Smithers Ursula Hades Morgana Ratigan Fidget King K.Rool Klump Krusha M.Bison Pinky and the Brain The Predator Stan Heff Magica De Spell Zira Nuka Dr Blowhole Plankton Shere Khan Pete Lord Rothbart Sir Ruber Carface Killer Cruella De Vil Captain hook Rasputin Joker Harley Quinn Penguin Two-Face Poison Ivy Riddler Mr Freeze the Fearsome Five Makunga Tetsie Raffish Raplh Weasel Mcgreed Messina El Surpremo Divatox Elgar Rygog Lord Zedd Rita Repulsa Goldar Kaput Zosky Duck Vader Sharptooth Red Claw Screech Thud Yzma BrerFox BrerBear Mirage Tyranno Clayton Ratcliffe Shan-Yu the Horned King Creeper the Evil Queen Heather Drake Achmed the Dead Terrorist Newman Darla Dimple The Fratellis (Ma Fratelli, Francis Fratelli, and Jake Fratelli), and Team Rocket (Jessie, James, and Meowth) are hearing those conversations while plotting to get their revenge on Littlefoot and the gang.
Oogie Boogie, Creeper, Ozzy, Strut, Ichy, Dil, Rinkus, Sierra, Red Claw, Screech, Thud, The Fratellis (Ma Fratelli, Francis Fratelli, and Jake Fratelli), and Team Rocket (Jessie, James, and Meowth) unexpectedly show up to kidnap Littlefoot and the gang, but Ash tells them that they never will. Oogie tells Littlefoot and the gang that they will battle on the middle of the ocean. Jesse, Nadine, Elvis, Littlefoot, Ash, Stan, Mickey, Bugs, Genie, Zazu, Ttark, Woody, Taran, Mikey, Scooby-Doo, and the rest get the whales away from the cove by stealing the boat belonging to Glen, Jesse's adopted father, and leading them out of the cove to safety, but are not able to save themselves when the tanker explodes and the oil in the water catches fire. The villains show up as Oogie told Littlefoot and the gang. Jack defeats Oogie Boogie by ripping of his skin, Genie uses his magical powers to scare away Ichy and Dil, Mickey, Donald, and Goofy beat up Pete, Cera headbutts Pete and Team Rocket into the sky, Littlefoot tells Ozzy, Strut, Red Claw, Screech, Thud, and The Fratellis to go back to where they came from, and Creeper wildly laughs away and flies on one of The Horned King's dragons. Their boat hits a rock and starts to sink while Glen, Annie, Randolph, Littlefoot's grandparents, Professor Oak, Ludwig Von Drake, Rafiki, Mr. Thicknose, and Dallben set out to find them in Randolph's boat while calling for help. Nadine, Elvis, Littlefoot, and the rest are lifted into a rescue helicopter summoned by Randolph's distress signals, but Jesse slips out of the harness when reaching for the rescue helper's hand and crashes into the water below. Gurgi decides to jump into the water to save Jesse, Littlefoot jumps into the water, too, Taran also falls into the water, and finally Brand jumps into the water to save Jesse. Nadine, Elvis, and the rest scream for Jesse, Littlefoot, Taran, Gurgi, and Brand and beg the helicopter to go back down, but the pilot says there's too much smoke and it's choking the engine and flies the chopper away. Jesse, Littlefoot, Taran, Gurgi, and Brand surface as the chopper leaves, but are unable to stay above water. They go back underwater and see Willy and Mo swimming towards them. He grabs onto his dorsal fin and Willy brings Jesse to surface. However, they are trapped in the middle of the flames, but Willy and Mo are able to swim under them, taking Jesse, Littlefoot, Taran, Gurgi, and Brand with him. Once they surface, they come upon Randolph's boat. Glen and Annie pull Jesse, Littlefoot, Taran, Gurgi, and Brand aboard and they thank Willy and Mo for saving their lives. Willy and Mo do not want to leave, but Jesse tells them they're okay so they can go. Willy and Mo still do not budge and Jesse, Littlefoot, Taran, Gurgi, and Brand look to Randolph for help who gives them a signal. Jesse, Littlefoot, Taran, Gurgi, and Brand understand what it means and pet Willy and Mo one last time before giving him a signal to swim away. Willy does and is later reunited with his family again and Mo says good-bye to Littlefoot before time-traveling back to Big Water. Later, the rescue workers bring Nadine, Elvis, and the rest to the boat where they are happy to see Jesse, Littlefoot, Taran, Gurgi, and Brand alive. Jesse and Nadine and then Jesse acknowledges Elvis. Orddu, Orgorch, and Orwen show up again to tell Littlefoot and the gang that they did a good job helping get along with his little brother Elvis and also that they have decided to reform themselves so they would remind Littlefoot and the gang that they can can come with them on some more adventures whenever Genie is with them and so are Taran, Eilonwy, Fflewddur, and Gurgi. Elvis tells him he has something for him and hands him a battered, folded up picture which Jesse unfolds and sees that it's a picture of him and his mother. Jesse is stunned and Elvis tells him that he had ripped the picture out of anger, but taped it back together for him. Jesse lets Littlefoot and the rest see the picture, too. Elvis starts to cry as he tells Jesse that their mother always felt bad about abandoning Jesse, something Jesse never knew. Littlefoot also says "I wish our dog friend Charlie was here to see this. Then he would be proud of what did on this journey". He thanks Elvis for the picture and for finally allowing him to put the past behind him and hugs him. When they part, Elvis asks where Willy, Little Spot, Luna, and Mo are and Jesse tells him that they are reunited with their mother again and Mo went back to Big Water. Elvis asks him how he knows that and Jesse grasps the orca necklace Randolph gave him and tells him that he knows. Jesse then starts whispering the prayer Randolph taught him two years before as the screen fades in on Willy and his family swimming and jumping in the sea. Littlefoot and the rest have invited Jesse, Elvis, Randolph, and Nadine to join them on some more adventures as their next guests, but that would be another story.
- Ash Ketchum, Pikachu, Misty, Brock, Togepi, Professor Oak, Celebi, Stan Marsh, Kyle Broflovski, Eric Cartman, Kenny McCormick, Ike Broflovski, Mickey Mouse, Donald Duck, Goofy, Ludwig Von Drake, Bugs Bunny, Daffy Duck, Genie, The Vultures (Buzzie, Flaps, Dizzy, and Ziggy), Jiminy Cricket, Zazu, Rafiki, Mr. Thicknose, Hyp, Mutt, Nod, Tricia, Pterano, Mo, Taran, Princess Eilonwy, Fflewddur Fflam, Gurgi, Dallben, Hen Wen, Doli, Orddu, Orgoch, and Orwen, The Goonies (Mikey Walsh, Brand Walsh, Mouth Devereaux,Data Wang, Chunk Cohen, Andy Carmichael, Stef Steinbrenner, and Sloth Fratelli), Esmeralda, Djali,Scooby-Doo, Shaggy Rogers, Fred Jones, Daphne Blake, Velma Dinkley, Slimer, Stay Puft, Rex, Woog,Elsa, Dweeb, Jack Skellington,Oogie Boogie, Creeper, Ichy and Dil, Pete, The Fratellis (Ma Fratelli, Francis Fratelli, and Jake Fratelli), and Team Rocket (Jessie, James, and Meowth) guest star in film.
- Like in Littlefoot's Adventures of Free Willy, Guido and Mo join Littlefoot and the gang in this film, although Mo is still with Willy the Whale and his family. In this film, Littlefoot's grandparents also join Littlefoot and his friends, although they're with Glenn and Annie, despite them joining Littlefoot and the gang in every Littlefoot's Adventures film from Littlefoot's Adventures of Circle of Life onwards. Cera's little sister Tricia will join Littlefoot and his friends for the first time ever in this film, so Jesse will meet Tricia for the first time and Cera will tell Jesse about when she used to be jealous when Tricia hatched back in The Great Valley.
- This film actually takes place after SpongeBob SquarePants Meets The Hunchback of Notre Dame, which explains Genie and The Goonies already knowing Esmeralda and Djali.
- The reason why Genie is in this film is because Simba, Nala, Timon, Pumbaa, King Julien, Maurice, Mort,Terk, Tantor, Louis, and King Louie are the only members of the Jungle Adventure Crew to guest star inPooh's Adventures of Free Willy 2: The Adventure Home and Jafar and Iago are the only Aladdin characters to guest star in that film.
- The reason why Zazu and Rafiki are in this film is because Simba, Nala, Timon, Pumbaa, Scar, and the Hyenas are the only Lion King characters to guest star in Pooh's Adventures of Free Willy 2: The Adventure Home.
- Jesse, Elvis, Randolph, and Nadine will become the next recurring characters of the Littlefoot's Adventures Series, alongside The Goonies and the four main characters from The Black Cauldron.
- This will be an NTSC film (taken from a VHS copy of the movie) with NTSC bits from The Land Before Timefilms, the Pokémon films, South Park: Bigger, Longer & Uncut, the Aladdin films, Mickey, Donald, Goofy: The Three Musketeers, Mickey's House of Villains, A Goofy Movie, An Extremely Goofy Movie, The Lion King 1 and 2, The Black Cauldron, The Hunchback of Notre Dame, The Goonies, the Scooby-Doo films,We're Back! A Dinosaur's Story, The Nightmare Before Christmas'Andre 1994'. And Many Other Movies
- Like BowserMovies1989's Pooh's Adventures films featuring Slimer and Stay Puft, this film will use the episodes of the animated TV series The Real Ghostbusters, not the live-action Ghostbusters film. This is because BowserMovies1989 and Yru17 thought it would make more sense for a Ghostbusters character to guest star in a crossover film as an animated character rather than a live-action character.
- This film actually takes place after Spyro and Friends Say We're Back! A Dinosaur's Story, which explains Rex, Woog, Dweeb, and Elsa already knowing Taran, Princess Eilonwy, Fflewddur Fflam, and Gurgi from that film onwards.
- Both The Land Before Time III: The Time of the Great Giving, A Goofy Movie, and Free Willy 2: The Adventure Home were released in 1995.
- Both the first three Pokémon movies and Free Willy 2: The Adventure Home were released by Warner Bros.
- In order to make this film appropriate for children under 17 the same way as Littlefoot's Adventures of Aladdin, Winnie the Pooh Goes to South Park: Bigger, Longer & Uncut, Pooh's Adventures of Stand by Me,Littlefoot's Adventures of Free Willy, and Littlefoot's Adventures of The Black Cauldron, all of the mature content will be removed from the South Park bits.
- During the scene where Rex, Woog, Elsa, and Dweeb introduce themselves to Jesse, he is in his younger voice being dubbed as Louie relying "I think my name is Jesse, but seeing you's giving me doubts about my brain. What are you guys anyway?", Elsa answers "Dinosaurs, actually.", and Jesse (still dubbed as Louie) replies "Dinosaurs, huh? You do got that look".
- During the battle between Jack Skellington and Oogie Boogie, Daphne is dubbed as Sally saying "Jack, look out!".