On first day of Autumn, Winnie the Pooh is ready for another fun-filled season to be with his very best friend, Christopher Robin. However, Christopher Robin is nowhere to be found, which causes Pooh to worry. After finding a blue honey pot with a sticky note next to it, Owl interprets the letter, informing Pooh and his friends, Piglet, Rabbit, Tigger, Eeyore, Mewtwo, The Good Fairy, Slimer, and Stay Puft that Christopher Robin has been taken to Neverland, where resides their old enemy, Captain Hook. Owl sends the group off on an adventurous journey into Neverland to rescue their friend.
Peter Banning is a successful corporate lawyer whose relationship with his family, especially his two young children Jack and Maggie is strained by continuous absences and broken promises. His wife Moira struggles to keep them together and grows frustrated at Peter for his callous behavior. The family flies to London to visit Moira's grandmother, Wendy Darling, who helped Peter find a family when he was a young orphan.
Upon arrival, they meet Pooh and the others who had just arrived and an old man who has "lost his marbles", Toodles, Wendy's first orphan. Peter, Moira, and Wendy attend a ceremony for the expansion of Wendy's orphanage. While they are out, Hook kidnaps the children, leaving a signed note. Wendy tells Peter that he is in fact Peter Pan and that his old enemy has returned and taken his children for revenge, but he fails to remember anything.
Tinker Bell appears before Peter that night and knocks him unconscious and flies him along with our heroes to a pirate port in Neverland. There he awakens in disbelief, and is discovered by Captain Hook, his second in command Smee, and Pooh's newest enemies, Bowser Koopa, Bowser Jr. and Mistress 9, who threaten the children unless he accepts Hook's challenge to a duel. Tinker Bell intervenes and is granted three days in which to prepare him for it. The Lost Boys, now led by Peter's replacement, Rufio, at first dismiss him as an old man who has no hope of regaining his former glory, but he begins to learn the magic of Neverland.
Meanwhile, Hook and Bowser uses Jack's frustration over his father's continuous broken promises to steal his affection. Peter is heartbroken when he sees Hook treating Jack like a son and becomes determined to win his family back. He finally remembers his past and learns how to fly by recalling his "happy thought": being a father. Peter regains the leadership of the Lost Boys and they challenge Hook and his pirates in an all-out battle. Peter regains Jack's love and saves Maggie, but during the fight Rufio is killed by Hook. Peter and Hook engage in a climactic sword fight, Hook is apparently killed when the Crocodile, now a massive clock tower, falls on him. Peter returns home with Jack and Maggie, Pooh and the others, and Christopher Robin and designates the largest member of the Lost Boys, Thud Butt, the only other lost boy besides Rufio whom Peter grew a connection to, as leader of the Lost Boys in his absence, and tells all the Lost Boys to take care of everybody smaller than them.
Returning home, Peter realizes the love he has for his family and the importance of having a youthful heart. Toodles, a former Lost Boy, is dismayed at missing the adventure, but discovers pixie dust in his bag of lost marbles and uses it to go flying around London and back to Neverland. Wendy remarks to Peter that his adventures are now over, but Peter says to live would be a great adventure too.
Some time later, Pooh heads over to see Christopher Robin, but only to be captured by General Grievous and Team Rocket, along with Piglet, Rabbit, Tigger, Eeyore, Mewtwo, the Good Fairy, Stay Puft, Ash, Misty, Brock, and Pikachu. Ash demands Grievous to let them out, only for the droid to tell that he will once they head back to Coruscant.
- Bowser, Bowser Jr., and Mistress Nine guest star in this film. Ash, Pikachu, Misty, Brock, Jessie, James, Meowth, and General Grievous guest star in the bonus ending of this film. Ash only has one speaking role saying "You better let us out of here right now!", Pikachu, Misty, and Brock don't have speaking roles, Jessie and James are only heard laughing, and also, Meowth and General Grievous have a few speaking roles and are heard laughing.
- After the credits, Pooh, Ash, and their friends are captured by Team Rocket and a new enemy called General Grievous and this is where Pooh's Adventures of Star Wars Episode III: Revenge of the Sith takes place. However, yru17 plans to make Pooh's Adventures of Star Wars: The Clone Wars, which may have to take place before the ending.
- Both The Real Ghostbusters And Hook Are Made Under License By Sony Pictures Consumer Products
- Although this film is an NTSC film with PAL bits from Pooh's Grand Adventure: The Search for Christopher Robin and Piglet's Big Movie, this is BowserMovies1989's first movie to use the PAL version of Pooh's Heffalump Movie instead of the NTSC version (due to the fact that the PAL version is the only version on YouTube).
- This is BowserMovies1989's first and only Winnie the Pooh/Steven Spielberg movie he ever made as of now.