An evil genius in a flying fortress is trying to kidnap the birds of the fire, ice, and lightning islands in hopes of luring the sea power, Lugia, and controlling the world. Ash and his friends, in the process of carrying out an island tradition that requires visiting those three islands, discover the plot and try to stop it. Even the comic villains, Team Rocket, turn good and help out in the end against the threat of world destruction. And Pokemon assemble from all around the world in case they can be of help (but they end up helping only the merchandising).

When Molly Hale's father goes missing, the strange Pokemon that he was studying come to Molly by the power of the strange little blocks. The Pokemon, the Unown, create Entei to act as Molly's father, and, because of her wish to have a mother too, Entei only goes and kidnaps Delia Ketchum, who just happens to be Ash's mom. So Ash, Misty and Brock go to the Hale mansion to stop these strange events once and for all...before time runs out for life as we know it.