The feature film focuses on the beautiful town of Greenfield. A resident of the town is Professor Spencer Hale, a research scientist who is researching 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 with her mother disappearing previously. Molly finds a box of tablets containing Unknown images and begins resembling the letters which summons the Unknown themselves. The Unknown 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. A fake Entei is created to represent Molly's father. Various people come to help sort out the Unknown, including Professor Oak and Delia Ketchum, Ash's mother.
Meanwhile, Ash Ketchum and his friends have landed 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. Through Entei's powers, Delia is hypnotized into thinking she is Molly's mother and ends up being kidnapped. 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 a Pokémon trainer named 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 and the others through a television and falls asleep, imagining herself being a Pokémon Trainer. Entei then creates a dream version of Molly, however she is an adult trainer, and takes her to battle the three. She first fights Brock but her dreamed-up Pokémon are stronger than his, and then she has a more friendlier fight against Misty in an underwater battle but the winner is not shown.
Ash manages to locate Molly and Delia, but Molly refuses to leave with him and the mansion transforms. Entei refuses to allow Ash to leave with his mother, and fights his Pokémon. He then blasts Ash and Pikachu off a cliff, but they are saved by the arrival of Ash's Charizard. Charizard with Ash on his back, battles Entei until he is knocked out of the sky. Entei nearly kills Charizard until Molly commands him to stop and begs that no more fighting happens, which manages to stop Entei. Ash and his friends convince Molly to leave with them, Entei revealing he was created by the Unknown to be her father.
The Unown suddenly lose control of their powers and start to seal the group in the mansion. Ash, Pikachu, Charizard, Misty, Brock, Delia, Molly and Team Rocket escape down to the hall where the Unknown are. Pikachu and Charizard attempt to break the forcefield protecting the Unknown, but they are joined by Entei, combining their powers to destroy the shield with Molly's support. Entei sacrifices himself and the Unown return to their dimension, reversing all of their effects on the world and returning Professor Hale to the ruins where he vanished.
The group venture outside where Professor Oak, Skyler, Lisa and others meet them. Team Rocket hide in the mansion upon seeing all of the police outside and vow they will succeed or fail in their next scheme. In the end credits, Charizard and Lisa depart from Ash's company, and Molly is seen with her own Teddiursa and is reunited with her father, and later, her mother.