Ash and the gang are headed to Fortree City when it starts raining and then snowing. They run for shelter and meet a Castform who leads them onward. The gang is greeted by two scientists from the nearby Weather Institute, Bart and Millie. Brock feels absolutely nothing for the attractive Millie, which puzzles him.

Millie is showing the kids around the Weather Institute when a Team Aqua helicopter suddenly appears, and they restrain all the other scientists (plus Team Rocket). Team Aqua is looking for information on the Legendary Pokémon, Groudon and Kyogre. Bart gives his access card to Castform, who flees in search of Millie.

Inside the institute, Ash, Millie and friends reunite with Castform, fight off Team Aqua, and use the access card to get into the computer. Millie transfers all the data onto a disk and deletes the copy on the hard drive.

Outside, Team Aqua uses the weather machine to create a bolt of lightning that sends Team Rocket blasting off. Millie gives Team Aqua the access card. A Team Aqua technician finds the files missing, and Millie reveals that she is in fact, a he—Brodie, the Man of a Thousand Faces, a member of Team Magma! He escapes with the disk.

Team Aqua leaves.  Bart is feeling betrayed, but then the real Millie shows up—and Bart puts her to work transferring all their paper files on the Legendary Pokémon back into the computer.