The feature film focuses on the beautiful town of Greenfield. A resident of the town, the research scientist Professor Spencer Hale, conducts research on the elusive Unown. He and his assistant, Skyler, discover a site of ruins, but Hale is sucked into the dimension of the Unown.
His disappearance leaves his young daughter Molly alone, her mother having disappeared previously. Molly finds a box of tablets containing Unown images and begins assembling the letters, which summons the Unown themselves. The Unown use their powers to make Molly's wishes come true, transforming her manor house into a crystal-like palace which spreads across the town and cuts her off from the world. Entei is created to represent Molly's father. Various people come to help sort out the Unown, including Professor Oak and Delia Ketchum (Ash's mother).
Meanwhile, Ash and his friends meet and befriend a trainer named Lisa. They come into Greenfield in the process and agree to join in the rescue mission to save young Molly. However, Entei kidnaps Delia, following Molly's request for a mother as well. Entei's powers hypnotize Delia into thinking she is Molly's mother. Ash, Misty, Brock and their Pokémon head out to the mansion to save Delia, communicating with Professor Oak and Skyler thanks to a PokéGear device given to them by Lisa. Team Rocket try to investigate the mansion, only to be blasted out of the air by Entei into the depths of the mansion. Molly watches Ash's Bulbasaur and Chikorita in action through a television and falls asleep, imagining herself being a Pokémon Trainer. Seeing Ash on TV, Delia snaps out of her trance, which is not noticed by Entei, who then creates a dream version of Molly as an adult and takes her to battle the three. Molly first fights Brock, but Molly's dreamed-up Pokémon are stronger than his; Molly then has a more friendly fight against Misty in an underwater battle, but the winner is not shown.