The movie begins in Tyler's House Where His Team Decided To Go To the Hundred Acre Wood where Winnie the Pooh, Ash Ketchum, and their friends preparing to celebrate a Halloween party at a fancy mansion called Crane Manor with Scooby-Doo and the Mystery Inc. gang.
Meanwhile, the raging Halloween party is happening at Crane Manor. Outside, in the foggy night, a horesman rides by, a grinning pumpkin for a head! Not far away from the house, Jafar, along with is parrot sidekick Iago , and the other villains Maleficent, Myotismon, Ursula, Hades, Dr. Facilier, Gaston, The Evil Queen, Scar , Cruella De Vil, and the Grand Duke of Owls plot their Halloween trick by crashing the party, taking over Crane Manor, and getting revenge on Pooh, Ash, and their friends for good. The mansion is the huge and studious Crane Manor, and Mystery Inc. has been invited by Mrs. Crane to the Halloween Party. Scooby Dum, Scooby's cousin, is also there with Mystery Inc. Fred, Daphne and Velma bob for apples and Shaggy and Scooby are hitting up the buffet table, as usual.
Scooby, Shaggy and Scooby-Dum encounter the Headless Horseman outside and run back inside to tell the others. Daphne, Fred and Velma (along with Pooh, Ash, Simba, Yakko, Fred Flintstone, George Jetson, Charlie Brown, Timmy Turner, and the others) are in the library with Mrs. Crane's niece, Beth. Beth mentions her great, great grandfather was Ichabod Crane. Scooby and Shaggy run in and tell their story, and Beth fears that the Headless Horseman has come back to haunt her family, considering her great, great grandfather Ichabod was chased by one years earlier. Tigger then tells a tale of how and the gang first faced the Horseman. Back on the party floor, the Headless Horseman, Jafar, and the other villains make an entrance causing havoc. The villains scares away the guests, but not the heroes.
The gang splits up to look for clues. Pooh, Piglet, Tigger, Roo, Lumpy, Ash, Pikachu, Tennessee, Chumley, Garfield, Odie, Poky , Shy, Tip, Dash, Lucky, Rolly, Cadpig, Spot, Timon, Pumbaa, Yakko, Wakko, Dot, Rocko, Heffer, Filburt, Baloo, Dino, Astro, Georgette, Charlie Brown, Linus, Snoopy, Woodstock, Timmy Turner, Cosmo, Wanda, Velma, Scooby, Scooby-Dum, and Shaggy search upstairs. They start looking into rooms, but find nothing. Velma returns downstairs and Pooh, Piglet, Tigger, Roo, Lumpy, Ash, Pikachu, Tennessee, Chumley, Garfield, Odie, Poky, Shy, Tip, Dash, Lucky, Rolly, Cadpig, Spot, Timon, Pumbaa, Yakko, Wakko, Dot, Rocko, Heffer, Filburt, Baloo, Dino, Astro, Georgette, Charlie Brown, Linus, Snoopy, Woodstock, Timmy Turner, Cosmo, Wanda, Scooby, Scooby-Dum, and Shaggy run into the villains who gives chase. Shaggy and the others run downstairs to tell the gang, but when they all return upstairs, the villains are gone. Mrs. Crane is nearly grabbed by the Horseman and the heroes tries to comfort her, when a man appears and explains that the Horseman is not after her head, but is after Mrs. Crane's necklace. Beth says this is her cousin Elwood. Elwood states that ever since Mrs. Crane brought the necklace into the house, Jafar, Iago, Maleficent, Myotismon, Ursula, Hades, Dr. Facilier, Gaston, the Evil Queen, Scar, Cruella De Vil, the Grand Duke of Owls, and the Headless Horseman have been appearing. Elwood makes an exit and the others get to work. Meanwhile, the villains meet Yakko, Wakko, and Dot's arch enemy Sordan Insane and agree that he can team up with them to do away with Pooh, Ash, and the others
Elwood takes Mrs. Crane's necklace to the bank and the gang watches him drive away, and witness the Horseman ride by and snatch Elwood's head off and place it on his own shoulders! The Horseman and the villains disappears afterwards. The gang looks around Elwood's wrecked car and finds a small picture of Elwood with glue on one side, the ignition keys missing, and a newspaper clipping that tells about a flying saucer spotted at a beautician's convention. They bump into Tarlof, Mrs. Crane's butler. He explains that someone chopped a tree down and it fell on the power lines cutting the power to the mansion, and he was walking to the neighbor's to complain. The gang goes to wear the Headless Horseman is supposedly buried. Fred and Velma figure it out and race to the airport. Sure enough, the Headless Horseman and the villains are there, about to take off in a plane. A battle follows with Ash and Brock using their Pokemon to defeat Hades. Timmy Turner battled The Duke and Tigger helps out by using a flashlight to scare the Duke away. Fred Flintstone, Barney Rubble, and Dino fought Ursula and Tigger told her to get lost, she vows that she'll get Pooh and the others next time. Simba fights off Scar. Charlie Brown and his friends defated Dr. Facilier's army of shadows while Baloo smashes the voodoo talsiman, causing Facilier's friends on the other side to drag the Shadow Man to the underworld again. Gaston captures Pooh and Ash, but is stopped by Pumbaa. Dot put a huge stack of dynamite into Sordan Insane's pants, causing them to blow him away. Garfield, Odie, Georgette, and Snoopy trick Cruella De Vil intro running her car through a machine and Tigger told her to get lost, and she vows she'll get even with Pooh and the others next time. Pooh uses Ice Cream to fight Jafar, Iago, Maleficent, and Myotismon, but he soon ran out of it. Aladdin makes a cameo and he gives his friends a magic lamp and Ash throws it to Pooh and Pooh uses the lamp to put the four villains in it. Tigger uses a caterpult to send the lamp far from the airport. The Evil Queen who appeares in her witch form captures Pooh and his friends, and is stopped by Pikachu's thundershock, causing her to plummet froma cliff. Scooby and Shaggy accidentally hop on the plane with the horseman and manage to elude him as the plane soars through the air. Finally the plane wrecks and the Headless Horseman is unmasked as Cousin Elwood. He was after Mrs. Crane's diamond necklace all along, so he made up the horseman to trick Mrs. Crane into believeing the necklace was cursed. Elwood was taken to jail by the Sheriff.
The clues are explained as well, the missing keys, Elwood grabbed them out of habit when he left the car, and the picture was a passport photo for Elwood to fly out of the country. And another thing, Elwood was lying when he said he called the bank, because the butler said the phone lines were down. Shaggy found the biggest clue; on the other side of the clipping, it reads that APEX, Elwood's shoe company, had filed for bankruptcy, so he tried to steal the diamonds.
In a bonus ending, Bowser Koopa was angry when he learned that Timmy Turner helped Pooh and his friends defeated the villains. Timmy's evil teacher Denzel Crocker arrives and informs him that Cosmo and Wanda are Timmy's fairy godparents. Bowser hires Mr. Crocker after he offered to team up to capture the fairy and seek revenge on Pooh and his friends before sending Icy, Darcy, and Stormy to bring back the villains who failed the mission. Meanwhile, Bowser talks to his secret master, the Ancient Minister, as they talk about how to outsmart Winnie the Pooh and his friends, making the Ancient Minister the new evil boss for the Pooh's Adventures series.
- Ash Ketchum, Pikachu, Misty, Brock, Togepi, Kanga, Roo, Lumpy, Tennesse Tuxedo, Chumley, Garfield, Odie, Poky Little Puppy, Shy Little Kitten, Tip, Dash, Lucky, Rolly, Cadpig, Spot the Chicken, Simba, Timon, Pumbaa, Yakko, Wakko, and Dot, Rocko, Heffer, Filburt Earthworm Jim Peter Puppy Princess What's-Her-Name Snott, Baloo, Fred Flintstone, Barney Rubble, Dino, George Jetson, Elroy Jetson, Astro, Georgette, Ttark, Charlie Brown, Linus Van Pelt, Lucy Van Pelt, Sally Brown, Schroeder, Peppermint Patty, Marcie, Violet Gray, Patty, Pig-Pen, Snoopy, Woodstock, Timmy Turner, Cosmo, Wanda, Chester, A.J., Elmer, Sanjay, Trixie Tang, Jafar, Iago, Maleficent, Myotismon, Ursula, Hades, Dr. Facilier, Gaston, The Evil Queen, Scar, Cruella De Vil, Sodarn Insane Demongo, and the Grand Duke of Owls guest starred in this Halloween movie.
- This film featured new versions of the songs "Perfect Isn't Easy " from Oliver & Company, "The Recycle Song " from Rocko's Modern Life, "Monster Mash " from Happy Haunting - Party at Disneyland, "The Headless Horseman Song " from The Adventures of Ichabod and Mr. Toad, "Friends on the Other Side" from The Princess and the Frog, "Be Prepared", from The Lion King, and "It's Our House Now!" Mickey's House of Villains.
- Buzz Lightyear made a cameo apperance in the movie.
- Aladdin also made a cameo during the battle scene.
- In one scene of the movie, Winnie the Pooh mentions Bloom's name when he wishes she and her friends were friends were there to help them set things right.
- The bonus ending of the movie featured Bowser Koopa, Bowser Jr., Mistress 9, the Trix The Psycho Rangers (Icy, Darcy, and Stormy) (in which the film took place after the first three Winnie the Pooh/Winx Club seasons), Denzel Crocker, and the Ancient Minister.
- This film is inspired by Pooh's Adventures of 101 Dalmatians and the Disneyland and Walt Disney World versions of Winnie The Pooh In Fantasmic!.
- This film takes place after Winnie the Pooh and The Adventures of Ichabod and Mr. Toad and Bloom and The Adventures of Ichabod and Mr. Toad, which explains Pooh, Ash, Simba, and their friends already facing the Headless Horseman.
- This film takes place after Pooh's Adventures of Oliver & Company, and Bloom's Adventures of Oliver & Company, which explains Pooh, Ash, Simba, Scooby-Doo, and their friends already knowing Georgette, and Georgette already facing Jafar, Iago, Maleficent, Ursula, Hades, Dr. Facilier, and the Grand Duke of Owls.
- This film takes place after Ash's Adventures of Beauty and the Beast, which explains Ash Ketchum, Tennessee Tuxedo, Scooby-Doo, and the their friends already facing Gaston.
- This film actually took place before Winnie the Pooh Says Hocus Pocus.
- This film featured a flashback from Pooh's Adventures of Beauty and the Beast, which showed how Pooh and his friends first met Gaston.
- The battle scene featured music scores from 101 Dalmatians, Star Wars, Aladdin, Sleeping Beauty, Animaniacs SNES video game, Oliver & Company, The Jungle Book, and Beauty and the Beast.