Jimmy has confronted Team Rocket agents Attila and Hun, who are about to capture Raikou with the help of the electricity-absorbing Miracle Crystal device. Attila and Hun send out Skarmory and Steelix, catching Typhlosion in a Sandstorm attack and hitting it with Steel Wing. Jimmy's friend Marina sends in her Misdreavus for support, and Jimmy sends his Beedrill to damage Attila's capturing robot. Team Rocket finally retreats, leaving behind the injured Raikou. But even though Jimmy just wants to help, Raikou won't let anyone get close until it finally collapses and is taken to the Pokémon Center.

Even at the Pokémon Center, Raikou resents being in captivity. A strange man in a cape runs in to see Raikou for himself—his name is Eugene, and although he promises to help protect Raikou, he knows it's suspicious of people. In fact, the next morning, Raikou breaks out of the Center as soon as it wakes up, and Eugene grabs Jimmy and Marina to follow it in his car. Team Rocket has set up another Miracle Crystal trap and Raikou is headed straight for it! Hun uses Steelix to provoke Raikou into using up even more electrical energy, but Jimmy, Marina, and Eugene are soon on the scene.

Steelix turns its attacks on the Trainers, but Jimmy and Marina's friend Vincent appears and saves the day with his Meganium. The Crystal's absorption powers have exhausted Raikou, but Typhlosion, Meganium, and Marina's Misdreavus can disrupt the Crystal's energy field if they all attack it at once. Despite their efforts, Attila quickly grabs Raikou and Team Rocket takes off. When the dust settles, Marina is missing as well! She was grabbed by accident, and now she's with Raikou in the cargo hold of Team Rocket's ship. When Raikou's struggles dislodge a floor panel, Marina disrupts the ship's wiring and opens the cargo hold doors. Raikou escapes, but Marina is still inside the ship... and Team Rocket knows exactly what's going on!