Professor Spencer Hale has been trying to uncover the secrets about a mysterious Pokémon known as the Unown that appear as twenty-six entities in the shape of the letters of the alphabet. Called to a recent discovery, Hale suddenly vanishes from the scene, leaving his young daughter, Molly, all alone in their expansive mansion.
Upset that her father has now disappeared just as her mother did two years ago, Molly is understandably distraught, and her strong emotions and tears activate the Unown that can read human minds and turn thoughts, dreams and desires into reality. Since she last equated her father to Entei, a leonine Pokémon that she read about from a storybook with him, that large creature suddenly appears and takes the place of her father, just as large crystalline structures encase the mansion, sealing Molly within her fantasy world.
With Molly desirous of having a mother as well, Entei leaves the mansion to find one, returning with Delia Ketchum, the mother of one of the most famous Pokémon trainers, Ash Ketchum. Seeing her abduction, Ash, his friends Misty and Brock, and their various Pokémon then set out to rescue Delia from her crystal prison, all while dealing with Molly who doesn't want her fantasy world disturbed, and Entei who will do anything to defend the girl and uphold her wishes.