The opening prologue starts in Hollywood, California, 1939, in which Danny sends out an invitation to Sawyer to be in the next Pooh play. The film fast forwards to the 100 Acre Wood 55 years later (1994), where Chistopher Robin does his usual running gag of introducing the film.
10-year-old pessimist Richard Tyler (Culkin) lives his life based on statistics and fears practically everything. His exasperated parents have tried multiple ways to build up the courage of their son, but to little success. And after Richard meets Alvin, Baby Bugs, Baby Kermit, Pooh and all the gang, they were sent by his father to buy a bag of nails so that he can build atreehouse. However, they get caught in not only in a harsh thunderstorm, but being chased by The Nostalgia Critic and they take shelter in a library. Here, they are met by Mr. Dewey, an eccentric librarian who tries to find a book for Richard and his friends and gives him a library card. However, Richard does not want any books; he just wants to call his parents and go home while the others point out that they want to get away from the Nostalgia Critic. Mr. Dewey points the boy towards a payphone. Richard wanders off and finds a large rotunda painted with classic fictional characters. Richard slips on some water that had dripped from his coat and falls down, hitting his head and knocking him unconscious. He awakens and finds the rotunda paintings melting, Maleficent appears and attempts to banish our heroes to the world of literature, forming a wave of color that transforms them and the library into illustrations.
Richard, Alvin, Baby Bugs, Baby Kermit, Pooh and all the others are approached by the Pagemaster who sends him on a journey into the fiction section to find the "exit". Along the way, Richard befriends three anthropomorphic books: Adventure, a swashbuckling pirate-like book; Fantasy, a sassy but caring fairy tale book; and Horror, a fearful "hunchbook" with a misshapen spine (in which Billy refers to Horror as "a turtle".). The three agree to help Richard to find his way out if he checks them out with his library card. Together, our heroes meet Tai, wargreymon, matt, metalgarurumon, Sora, Biyomon and many more. Unfortunately, they lost The Tiny toons, Spyro and his team, and Batty in the process. At the other side, The Nostalgia Critic got through the world of literature. They encounter classic-fictional characters. They meet Dr. Jekyll, in a haunted house where he transforms into the monstrous Mr. Hyde (which Billy mistaken him as a Chilaula), and faced The Nostalgia Critic, who turns out to have been Myotismon in disguise, before heading out into open waters to the Land of Adventure. However, the group are separated after an attack by Moby Dick. Richard, Adventure, Alvin, Baby Bugs, Baby Kermit, Pooh, Piglet, Eeyore, Billy, Danny, Sawyer, Dave Felis, Renamon, Sora, and characters are left alone, which leaves Sora explaining about the 9/11 incident. Pooh thought of the idea for them to live in Skull but when he said they are a family, Dave's expression changed as he said that they're family but no his, which leads to him telling them the story of his hatred past, his mother's hatred to him for endangering his sister, making him leave to be a loner for causing nothing but death, Pooh said that he can come to our adventures anytime which Dave agrees to it. And after being annoyed by Billy's bagpipes, they were picked up by the crew of the Hispaniola, captained by Long John Silver. The pirates go to Treasure Island, but find no treasure, nearly causing a mutiny between the captain and crew. Tigger, Rabbit, Tai, Wargreymon, Matt, Metalgarurumon, Batty, Godzilla, Fantasy and Horror appear and defeat the pirates with the help of Timmy and Jenny. Silver attempts to take Richard with him, but he retreats when Richard threatens him with a sword. Adventure insults Horror, causing the hunchbook to get captured by Lilliputians from Gulliver's Travels. Adventure saves him and they make up.
As the group travels through the fantasy section Richard sees the exit sign on the top of a mountain. However, a sleeping Dragon is awakened and Myotismon use it to chase Richard and his friends. Richard fights the dragon off with a sword and shield, but it is in vain as the dragon wraps its tail around him, shaking his armor and weapons off of him before swallowing him whole. Richard finds books in its stomach and uses a beanstalk to escape and MetalGarurumon defeated Myotismon. our heroes arrive at the top and enter a large dark room where the Pagemaster awaits them. Richard berates the Pagemaster for the horrors they has suffered and how annoyed he was from being annoyed by Billy, but the Pagemaster reveals that the journey was intended to make Richard and the others to face their fears, while the others who left Pooh and the others behind like the Tiny Toons, Godzilla, Batty, Spyro, Sparx, Hunter and Bianca were returned home early. Meanwhile, Timmy and Jenny marry. The characters Richard had met beforehand reappear in a magical twister congratulating him. The portal opened for Richard and the others to return home. Richard and the others awaken, discovering that they had been unconscious all along. Adventure, Fantasy, and Horror appear next to his body as real books. Mr. Dewey finds him, and, even though the library policy only allows a person to check out two books at time, Dave asked Mr. Dewey to check out Horror, and he did. Richard and the others return home braver than before, sleeping in his new treehouse. Adventure, Fantasy, and Horror appear as silhouettes on a wall talking, Adventure gets kissed by Horror (or Billy) unintentionally off-screen.
- This film is a replacements for Chipmunks Tunes Babies & All-Stars' Adventures of The NeverEnding Story III: Escape from Fantasia since Cartoon All-Stars's Heroes Fantasy Films cancelled it.
- DaisyHead Mayzie, the Weekenders, Pelswick and his friends, Crazylegs Crane and Dragonfly, Coconut Fred and his friends (from Coconut Fred's Fruit Salad Island), Yakkity Yak, Keo and Lemony (from Yakkity Yak), Wall-E and Eve, Spider and Fly , Earl and his Family, Roy (Earl's Friend), the Tiny Toons Gang, Blard Simpleton, Simba, Timon, Pumbaa, Ttark, Rocko, Heffer, Filburt, Baloo, Fred Flintstone, Scrappy-Doo, Scooby-Dum, Jack Skellington, Thomas the tank engine and his friends, the Sesame Street gang, Arthur and his friends, D.W., Emily, the Tibble twins, Mr. Ratburn, Godzilla, Godzooky, Little Godzilla, Minilla, Anguirus, Rodan, Mothra, Jet Jaguar, Moguera, Napoleon, Birdo, Dennis the Menace and his friends, the Kids Next Door, Numbuh 362, the Mighty Morphin Power Rangers, Alpha-5, Zordon, Dink the Little Dinosaur and his friends, Courage the Cowardly Dog, Princess Aroura, Prince Phillip, Samson (Prince Phillip's Horse), Flora, Fauna, Merryweather, Clifford the big red dog, Cleo, T-Bone, Mac, Emily Elizabeth, Jetta, Charley, Sharon Spitz and her friends, Super Why and his friends, the Word World gang, Sailor Moon and the Sailor Scouts, Skunk, Fox, Rover Dangerfield and his friends, Balto and his friends, Frank Phil, Oobi, Uma, Kako, Grampu, Wicket the Ewok, Princess Kneesa, Teebo, Latara, Princess Merida, Lloyd and his Friends (from Lloyd in Space), King Russle and his Friends (From King), Guile and the Street Fighters, Peter Rabbit, Norman (from Paranorman), Johnny Test, Dukey, Mary Test, Susan Test, Otto Rocket and his Friends (from Rocket Power), Saber Rider and the Star Sheriffs, Captain N and His Friends (from Captain N the Game Master), Arthur (from Arthur Christmas), Donkey Kong, Diddy Kong, Ariel and her family (including Princess Melody and King Triton), the Blue's Clues gang, Ace Bunny and his friends
- Myotismon appear in the Fantasy section
- Tai, wargreymon, matt, metalgarurumon, sora, biyomon, and baty live in skull with pooh at the end of the film.
- The song "Something Better", from "Muppet Treasure Island" appears on the end credits.