The film begins with Christopher Robin Milne introducing the play taken from the episode "Paw and Order".
It is winter-time in Paris and the girls all set off at half-past nine in two straight lines, as part of their usual routine. Then the girls reunites with Winnie the Pooh, Piglet, Tigger, Rabbit, Eeyore, Ash, Pikachu, Misty, Togepi, Brock, Yakko, Wakko, Dot, The Vultures, and Jiminy Cricket, and they introduces them to Kanga, Roo, Lumpy, Zazu, Littlefoot, Cera, Ducky, Petrie, Spike, Mickey, Donald, Goofy, SpongeBob, Patrick, Scooby, Shaggy, The Penguins, King Julien, Maurice, Mort, Terk, Tantor, Louis, Roger Rabbit, and Genie. However, the girls and Pooh and friends soon learn that Miss Clavel has a cold, so they wait for Dr. Chon to come and treat her. Meanwhile, Miss Clavel is interrupted by Pepito, who is practicing the violin next door. He promises Madeline and Pooh that he will not play again until Miss Clavel is well again. Dr. Cohn says for the girls and Pooh and friends to give Miss Clavel love and warmth, and that soon she shall be well. That night, the girls reminisce on the happy times they have with their families at home, like at times when they too are sick, Madeline tells them of the times she spent with her parents, but sadly she no longer has them to turn to, thus believing she has no family left. Heartbroken, the girls wail at Madeline's story, but are soon comforted by Miss Clavel and Pooh and friends, who has awoken by the noise. Pooh and friends and Miss Clavel reminds the girls that they all love and look out for each other, and that they all are just as much a family as anybody else, bringing peace of mind to all of the girls. Everybody returns to bed with sweet dreams.
After Miss Clavel feels better, a letter is delivered to the house, saying Madeline's long-lost Uncle Horst from Vienna is coming for a vist. Ecstatic that she still has a family, Madeline eargerly awaits his arrival. Uncle Horst arrives later in the week, and is reacquainted with his niece, whom he remembers fondly. Madeline and Pooh and friends are pleased to meet him, and Horst presents all twelve girls lace collars as a gift. Uncle Horst then announces that he has been made Madeline's new legal guardian, and that she is to accompany him to his hometown of Vienna, where Madeline can attend a fine finishing school. Although nobody wants her to leave, Madeline reluctantly agrees to go.
That evening, Uncle Horst returns to dine with the girls and Pooh and friends, as well as Lord Cucuface and Pepito's family. At dinner, Horst tells of the Austrian School to the girls, certain that it will be more fulfilling than Madeline's current school. The girls, wanting to prove that their home is just as good, puts on a musical to display their talents to Uncle Horst. Horst, however, does not sway from his intent and informs Madeline that they leave the next morning, while assuring her that she will come to love Vienna. Uncle Horst leaves for his hotel that night, during which Lord Cucuface reminds him of Madeline's inheritance, which Horst says he will be responsible for.
The night before Madeline was to leave with her uncle, Pepito tried and failed to stop the sun from waking up by preventing the rooster from doing his morning crowing. Soon Madeline leaves with her uncle for Gare de I'Est where the Orient Express will take them to Vienna. Before leaving, Miss Clavel gives Madeline her mother's beaded necklace, which she was to give Madeline "at the right time". The two then depart for Vienna, with Pooh and friends following them from a distance. However, the man though to be Madeline's uncle instead took her on the Paris Metro and to an unfamiliar part of town, even abandoning her pet dog Genevieve on the way, Pooh and friends who are still following fells something is wrong and follows after them by using a train they found and borrowed from (The Train from "The Good The Bad and The Tigger), but when Tigger was eating a banana he throw the banana peel on the tracks which causes the train to crash. Meanwhile Madeline fears that she is being kidnapped, Madeline throws pieces of her necklace to make a trail to where she is taken to. Madeline is soon taken to a lace store run by Madame LaCroque, where Uncle Horst accidentally reveals that he is French, not Viennese German as he had clamied. It is then revealed that Horst isn't her uncle at all, but a man named Henri, a failed Shakespearean actor. Inside are girls who were also kidnapped and were forced into making laces to sell. One of the girls, Fifi, befriended Madeline, Pooh and friends who saw the whole thing were discovered by LaCroque and Henri and locked the friends in a room. In the room, they were confronted by Bowser Koopa, Jafar, Iago, Maleficent, The Grand Duke of Owls, Hades, Ursula, The Joker, Harley Quinn, Dr. Facilier, Sheldon J. Plankton, Drake, Lord Rothbart, Scar, Sharptooth, and the Fossa. They told the friends that LaCroque and Henri are working for Bowser Koopa and she promises that she is done with the girls she will give them all to Bowser and work for him as his personal slaves and they cannot interfere and plans to hang Pooh and friends sometime later.
Shortly after Madeline and Pooh and friends left, Miss Clavel, the girls, and Pepito tried to stop her and Horst so that Pepito could give her his parting gift: A shrunken head from Brazil. They arrive at the train station, only to learn that the two had taken the Metro, not the Orient Express. They also find Genevieve abandoned at the statio, and can't find Pooh and the others anywhere. Fearing the worst, Miss Clavel enlists the police to help them rescue Madeline, Pooh, and the others.
Meanwhile, at the lace shop, Fifi's cough turns one of LaCroque's laces yellow, and she banned her from using white lace, and must instead make black lace in the dark. Madeline and Pooh and friends defend her, only to be thrown into the detention room. Fifi tells Madeline and Pooh and friends of how LaCroque was once a cabaret dancer who had once torn her dress and fell off stage when performing. In total humiliation, she refused to perform, and sold her long hair to make lace. She then went into the lace business and kidnapped all of the girls to work as her miserable servants.
Meanwhile, Pepito and Madeline's friends go off to find her and Pooh and friends on their own and discover the trail of beads that led to the lace store. A customer claims to LaCroque she wants red lace, which gives her the idea to cut off some of Madeline and Misty's hair, Meanwhile upstairs Bowser demands to have Pooh and friends hanged immediatley.
Madeline, Pooh, and the others tells there new friends when an escape plan fails that they may be small, but can follow as one. LaCroque and the others interrupts and cuts off some of Madeline and Misty's hair and Bowser and the villains is about to bring Pooh and friends to the back to be hanged, while Pepito is able to swipe off LaCroque's wig while outside the window. Miss Clavel and the police were able to discover the so-called uncle after a boy trips him after refusing to give any change.
While Madeline, Pooh and the others is still in the lace factory, Pepito and the girls use the shrunken head to knock off LaCroque's wig, and then Ash uses Charizard to frighten her to the ground. Meanwhile, Miss Clavel is able to convince Henri to lead them to Madeline and Pooh and friends by telling him "Surely, if you help, the cops won't be so hard on you." Henri reluctantly agrees to lead them there.
Madeline, Pooh and the others and all of there friends are able to tangle LaCroque in lace just as the police car pulls up. Henri, feeling guilty, tries to escape, only to be tripped by Scooby's Tail, allowing the girls to tangle him up as well. LaCroque accidentally kicks Henri during the chase, just before she trips. She and Henri are arrested by the police and taken to jail. But then The Duke comes up from behind Madeline and chokes her, Pooh and friends comes up to Madeline, only to find her unconscious. Saddened by this Pooh and the others started to fight Bowser and the other villains. Ash and Brock use their Pokemon to defeat Hades. The Vultures attacked the Duke and Shaggy and Scooby helps out buy using a flashlight to scare the Duke away. Tigger and Pikachu fights Ursula and they told her to get lost, she vows that she'll get Pooh and the others next time. Lord Rothbart was defeated by a well-aimed torpedo, which SpongeBob and Patrick had propelled. Genie defeats Sharptooth by turning him into a small lizard and flung him far from Paris. Tantor shots Plankton far way from here. Drake was defeated by the combined might of Mickey, Donald, and Goofy. Dr. Facilier was defeated when Littlefoot destroys the charm which causes the voodo spirits to drag him to the voodo version of hell. Scar was defeated when Cera charges at him sending him flying far from her. King Julien uses conga dancing to defeat The Joker and Harley Quinn. Dot Warner scares the Fossa by giving them the angry eyes. Pooh uses Ice Cream to fight Jafar, Maleficent, and Iago but he soon ran out of it. Aladdin makes a cameo and he gives Ash a magic lamp and Ash throws it to Pooh and Pooh uses the lamp to put the three villains in it. Tigger uses a caterpult to send the lamp far from Paris. After the battle Bowser escapes through a warphole. As Pooh and friends celebrate they notice Madeline still didn't wake up. As everyone sadly gather around Madeline, She wakes up and everyone rejoice and as are heros celebrate they realized the other factory girls are sad, because they still have no home. Madeline and Pooh has a great plan, though.
Madeline, Pooh, and friends receives a huge reward after returning home because of their work, and used it to open a school for orphaned girls and Madeline realizes that she has a family all around her. Pooh and friends and all of the girls from both schools rejoice in the fact that they are all truly a happy family.
- Christopher Plummer as The Narrator/ The Grand Duke of Owls
- Jim Cummings as Winnie the Pooh
- John Fiedler as Piglet
- Paul Winchell as Tigger
- Ken Sansom as Rabbit
- Peter Cullen as Eeyore
- Tim Koskins as Christopher Robin
- Nikita Hopkins as Roo
- Kath Soucie as Kanga
- Kyle Stranger as Lumpy
- Hal Smith as Owl
- Micheal Gough as Gopher
- J. Pat O'Malley as Buzzie the Vulture
- Chad Stuart as Flaps the Vulture
- Lord Tim Hudson as Dizzy the Vulture
- Digby Wolfe as Ziggy the Vulture
- Cliff Edwards as Jiminy Cricket
- Rowan Atkinson as Zazu
- Veronica Taylor as Ash Ketchum
- Ikue Otani as Pikachu
- Rachael Lillis as Misty
- Eric Stuart as Brock
- Satomi Korogi as Togepi
- Rop Paulsen as Yakko Warner/ Spike
- Jess Harnell as Wakko Warner
- Tress MacNeille as Dot Warner
- Cody Arens as Littlefoot
- Anndi McAfee as Cera
- Aria Curzon as Ducky
- Jeff Bennett as Petrie/ Kowalski
- Wayne Allwine as Mickey Mouse
- Tony Anselmo as Donald Duck
- Bill Farmer as Goofy
- Tom Kenny as SpongeBob SquarePants
- Bill Fagerbakke as Patrick Star
- Scott Innes as Scooby-Doo and Shaggy
- Tom McGrath as Skipper/ The Fossa
- James Patrick Stuart as Private
- John DiMaggio as Rico
- Danny Jacobs as King Julien
- Kevin Micheal Richardson as Maurice
- Andy Richter as Mort
- Rosie O'Donnell as Terk
- Wayne Knight as Tantor
- Michael-Leon Wooley as Louis
- Charles Fleischer as Roger Rabbit
- Robin Williams as Genie
- Harvey Atkin as Bowser Koopa
- Jonathan Freeman as Jafar
- Gilbert Gottfried as Iago
- Eleanor Audley as Maleficent
- James Woods as Hades
- Pat Carrol as Ursula
- Mark Hamil as The Joker
- Arleen Sorkin as Harley Quinn
- Keth David as Dr. Facilier
- Doug Lawrence as Sheldon J. Plankton
- Tim Curry as Drake
- Jack Palance as Lord Rothbart
- Jeremy Irons as Scar
- Frank Welker as Sharptooth/ Genevieve
- Fred Tatasciore as The Fossa
- Jerry Orbach as Pepe Le Pew
- Andrea Libman as Madeline
- Jason Alexander as Henri aka "Uncle Horst"
- Lauren Bacall as Madame LaCroque
- Stevie Vallance as Miss Clavel
- Brigid Tierney as Fifi
- Alex Hood as Pepito
- Susan Silo as Lord Cucuface
- Ash Ketchum, Pikachu, Misty, Togepi, Brock, Yakko Warner, Wakko Warner, Dot Warner, Littlefoot, Cera, Ducky, Petrie, Spike, Mickey Mouse, Donald Duck, Goofy, SpongeBob SquarePants, Patrick Star, Scooby Doo, Shaggy Rogers, The Penguins of Madagascar, King Julien, Maurice, Mort, Terk, Tantor, Louis, Roger Rabbit, Genie are the good guy guest stars of this film.
- Bowser Koopa, Jafar, Iago, Maleficent, The Grand Duke of Owls, Hades, Ursula, The Joker, Harley Quinn, Dr. Facilier, Sheldon J. Plankton, Drake, Lord Rothbart, Scar, Sharptooth, and the Fossa are the bad guy guest stars of this film.
- This film is a request from me Toonking1985.
- This film features battle music from Star Wars Episode I: The Phantom Menace (composed and conducted by John Williams), The Emperor's New Groove (composed and conducted by John Debney), 101 Dalmatians (composed by George Bruns), The Land Before Time (composed by James Horner), Aladdin and Beauty and the Beast (both composed by Alan Menken) have been used in the battle between good and evil.
- The film is inspired by Disneydaniel93's classic film Pooh's Adventures of 101 Dalmatians and also Winnie the Pooh in Fantasmic.
- Aladdin makes a cameo during the battle scene.
- Pepe Le Pew appears in a bit part, dressed like a police officer, who tries to help Miss Clavel find Madeline, Pooh and the others.
- Owl and Gopher also makes an appearance in this film from the beginning, the middle and to the end.
- In the scene where Pooh and friends uses a train to follow Madeline's train, Tigger said we borrowed the train from some one named Casey. It could be possible that Tigger borrowed the train from Casey Jones.
- The scene where King Julien uses the Conga dance to defeat The Joker and Harley Quinn is a reference to how King Julien defeats Arthur and Cecil by using the conga dance in Simba Timon and Pumbaa's adventures in Aladdin and The King of Thieves.
- Bowser Koopa in this film is potrayed more darker, sinister, ruthless, cold, and violent then his other early appearances.
- This movie is rated PG for language and action during the villains scenes.
- It is revealed that Genevieve is Scooby's half-sister.
- That's What Friends are For - The Vultures, Madeline, and the others
- Family - Madeline, Pooh and friends & 11 Little Girls
- We Can Sing, We Can Dance - 11 Little Girls, Pooh and friends, Uncle Horst and more
- Im Looking, Looking, Looking For You - from Super Mario World Show (plays during Pooh and friends chase after the train that Madeline is on)
- Something is Not Right - Miss Clavel, 11 Little Girls, Pooh and friends, Madeline and Uncle Horst
- Where is the hope that I once knew? - Madeline & Laceshop Girls
- Together - Madeline, Pooh and friends, & Laceshop Girls
- Family (reprise) - Madeline, Pooh and friends, 11 Little Girls & Laceshop Girls
- That's Why We're Here - Pooh and friends