The game begins in the player's bedroom as Jiminy Cricket hosts a storytime session consisting of Snow White and the Seven Dwarfs, Dumbo, Alice in Wonderland, and Peter Pan. He soon gets bored reading the same stories he has read several times before, and decides to instead makes things more "interesting": he rips the last pages of the tales and challenges the player to match each story with its ending. However, a storm rages in the room shortly afterwards that shows visions of the stories' villains - The Evil Queen, the Ringmaster, the Queen of Hearts, and Captain Hook - who attempt to grab the end pages before Jiminy shuts the book. The Blue Fairy then appears and warns Jiminy that by ripping out the happy endings, the stories were left unresolved, allowing the respective villains to take over and rewrite their respective stories to ensure their victories over the heroes. The Blue Fairy transforms the book's cover into a portal, allowing Jiminy and the player to venture into the stories to restore the happy endings and make amends.
Each story and their worlds have been drastically altered by the villains;
Snow White and the seven dwarves have been imprisoned by the Evil Queen and The Prince does not exist to awaken Snow from the sleeping death curse. The Queen forces Snow into eating her poisoned apple and then proceeds to put the dwarves to sleep as well: the player must brew some potions in order to make the Prince come back and kiss Snow White.
Dumbo is forced to perform a humiliating high dive act over and over to entertain the villainous audience and his mother Mrs. Jumbo is tied up beneath the circus ring: by influencing the clowns' sketch, the player makes them humiliate themselves, so Dumbo regains self confidence and flies again.
In Wonderland, Alice has been beheaded by the Queen of Hearts and her head separated from her body, but still alive and speaking, so the player, Jiminy, and the White Rabbit have to reunite them and then escape the Queen's hedge maze.
Peter Pan has become a decrepit old man and can't win a duel against Captain Hook. The player takes up Peter's sword and duels Hook and his pirates until he falls off his ship into the sea.
After restoring the true endings, the player and Jiminy are confronted by the four villains who invade the player's bedroom and each take one of the happy ending pages. The player uses the storybook as a shield, systematically destroying the villains' forces by reflecting them their own attacks until they are defeated. The Blue Fairy finally returns, adding a new tale to the book called "A Villain's Night Out" that describes the events of the game.
If the player adds magnesium sulfate instead or rose petals, the musician Prince appears instead.
The doorknobs on the storybook (Out and In) look exactly like the one from Alice in Wonderland.
Peter Pan's weapon of choice is commonly a dagger: here instead it's a long rapier, like Hook's (albeit without the golden guard).
According to concept art, Stromboli was going to be a villain in the game in a Pinocchio-based world but he was replaced by the Ringmaster. The reason of this is unknown, considering that Jiminy Cricket and the Blue Fairy are already present as main characters in the game and Stromboli is certainly far more evil than the Ringmaster.
