While studying over Pikachu's battles, Team Rocket is intruded by a mysterious woman calling herself "Madame X" along with her Pokémon Malamar, who takes interest in Ash's Pikachu. She gets Malamar to hypnotize Team Rocket to be her servants besides Meowth who escapes by using his fury swipes on himself to avoid being hypnotized. After meeting up with Ash and his friends, he warns them of what's going on until the rest of Team Rocket catch up to them, along with Madame X and Malamar. Pikachu is kidnapped and taken back to Madame X's hideout, so Ash and friends catch after them with a Pikachu tracking robot made by Clemont which eventually blows up. Once in the hideout, the gang splits up to look for Madame X. Malamar catches Clemont and Bonnie and hypnotizes them to go after Ash, Serena and Meowth. Malamar then catches up to them and tries to hypnotize the rest of the group. Ash gets Meowth to use fury swipes on him to avoid being hypnotized, but Serena doesn't want her face getting scratched and ends up getting hypnotized.

Ash, you, and Meowth split up as Clemont, Bonnie, and Serena search for you three by the orders of Madame X

Serena: Come on out… all Madame X wants is your pokemon and loyalty… she says as she walks down the halls of the old lab searching for you