With their friend Marina in Team Rocket's clutches, Jimmy and Vincent are in a panic. Jimmy remembers that Vincent can call Marina on her Poké Gear, but Hun has already taken it from her. However, Vincent can still trace the call to find Marina, and not a moment too soon: Team Rocket is setting up another Miracle Crystal trap for Raikou. Jimmy, Vincent, and Eugene find Team Rocket only moments before Raikou does, and this time, Raikou pounds the area with lightning while staying out of the Crystal's range. In the Chaos, Jimmy sends his Beedrill to rescue Marina by flying her out of Team Rocket's grasp.

Raikou purposely smashes the Crystal's control unit, but Team Rocket still doesn't look beaten. With the controls gone, the Crystal is on auto-destruct mode, sucking in energy until it explodes—and it latches onto Raikou, leaving it helpless! Eugene has a risky idea: break open the Crystal's field to rescue Raikou before the Crystal can explode. Jimmy's Typhlosion, Vincent's Meganium, and Marina's Misdreavus all volunteer to take the risk, and they charge the Crystal's energy field. At the same time, Eugene sends out his Alakazam to watch their backs, and Team Rocket sends out a Muk to make the battle even harder!

Even as Hun's Steelix attacks the Trainers, they order their Pokémon to concentrate on saving Raikou. Jimmy manages to trick Steelix into falling off a cliff, but it soon comes roaring back out of the ground! It lunges at the Pokémon trying to free Raikou, but Jimmy, Marina, and Vincent throw themselves in front of their Pokémon to protect them. When Raikou sees this, it blasts its way out of the Crystal's energy field to stop Steelix, then breaks the Crystal into pieces as Team Rocket flees for good. Raikou seems to realize that some people don't mean it any harm, and as it returns to the wild, Jimmy waves goodbye—as a friend!