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.
Ash and his friends continue towards Fortree City. The sunny day quickly turns to a torrential rainstorm and finally snow. After peculiar Pokémon floats in, Ash checks it out on his Pokédex and learns that it is a Castform, the Weather Pokémon. As Castform begins to lead the group to safety, the weather turns sunny again and Castform's form changes with the weather. Castform leads them to its Trainer, Bart, a researcher at the Weather Institute, and Bart's trainee, Millie, who has a Ditto. Brock, enters into his pretty-girl-trance at the sight of Millie, but unexpectedly he stops his flirting and can't quite explain it. Meanwhile, Team Rocket is snowed in, and appear to be enjoying themselves. Or at least Meowth is; Jessie and James blame the crazy weather patterns on Ash and his friends.
Bart escorts the group to the Weather Institute, and explains that their giant satellite dish was responsible for the changing weather condition. At her boss's request, Millie takes the group on a guided tour of the facility. Team Rocket later spot the satellite and immediately make ill-fated plans to use it for nefarious ends. Team Aqua fly onto the scene soon afterwards, and in full force, also after the Weather Institute’s technology. Shelly and her grunts capture the researchers and Rocket trio, clamped in metal restraints. The trio escape their restraints by sucking in their stomachs, though their blabbering annoys Shelly. Team Aqua begins powering up the weather control machine, summoning a lightning storm. Bart quickly realizes Team Aqua interest in the Legendary Pokémon data, so he hands the data Pass Card to Castform and orders it to go to Millie. Castform ducks into a ventilation shaft with Team Aqua in pursuit. Ash, his friends, and Millie are watching action outside on security cameras. As Ash sprints into action, Millie points out that all the air ducts lead to the room they are currently in and correctly predicts that Castform will come to them, but two Team Aqua grunts soon arrive and spot Castform. Everyone but Ash and Pikachu flees, and Pikachu knocks out the grunts with a Thunderbolt.
Millie suggests that they delete the data from the main computer, but it's being guarded by Team Aqua. Millie's Ditto Transforms into Castform and lures the Aqua guards away. Millie copies the data onto a disc and erases the master file. Meanwhile, Ash finds Ditto, who is still disguised as Castform, and carries it back to his friends and Millie, inadvertently leading the guards back to them. Ash calls out his Torkoal to provide a smokescreen. The group exit the Institute only to run into Team Aqua and their leader. Shelly has the weather control machine brought online and threatens the captured scientists with a lightning storm unless Millie turns over the key card. Team Rocket are blasted off by a lightning bolt. Bart, unaware that Millie has deleted the data, begs her not to give in, though Millie hands it over. Ash and friends grin as Team Aqua soon discovers that the data has been destroyed. Then Millie taunts Shelly with the data disc and jumps to the top of the machine. Everyone looks at her, surprised as "Millie" is revealed to be Brodie, a male member of Team Magma known for being a master of disguise. This explains Brock's lack of a reaction earlier.
Shelly orders her Crawdaunt to attack, though Brodie has Ditto quickly transform into a Crawdaunt. May gets involved in the battle, but Combusken is quickly taken out by a Crabhammer from Ditto. Brodie uses a jet pack and promptly escapes with the data and, for a change, the bad guys win this round. Shelly declares that she looks forward to defeating Team Magma next time before she and her grunts pull out. Afterwards, Bart is saddened that the Institute's data has been stolen and that "Millie" wasn't such a model employee afterall. The real Millie arrives on the scene, all ready for her first day. Brock does his patented flirting, though Max pulls him away. Bart quickly puts Millie to work, showing her to a chaotic study, where he asks her to manually re-enter all of the stolen data into system. Millie gladly accepts the large data entry task.