While taking a little time off on their way to Sunyshore City and Ash's next Gym Battle, our heroes discover Team Rocket's Meowth. The dazed Pokémon has been separated from Jessie and James after a rough run-in with Team Galactic! After explaining the situation, Meowth and our heroes head out to Team Galactic's secret base to rescue Jessie and James, as well as Looker from the International Police.

As Team Galactic continues to put the pieces together to accomplish its evil plans, our heroes confront the mysterious Jupiter of Team Galactic. She informs them she is aware of their previous encounters with the three lake Pokémon Mesprit, Azelf, and Uxie. This news bewilders our heroes all the more. Meanwhile, the gang (along with Meowth) rescues Looker, who has been trapped in a cell with Jessie and James. Team Galactic gets away, leaving Looker and our heroes still wondering what the evil organization is up to.

While trying to unravel the mystery, Looker discovers an object left behind by Team Galactic that, upon examination, destroys every bit of data the International Police have collected on them! That leaves everyone frustrated, but doubly determined to get to the bottom of Team Galactic's evil plans, as Pokémon Hunter J prepares to catch the very same three lake Pokémon...