A young Trainer named Jimmy and his Typhlosion are on a Pokémon journey, and their latest Pokémon battle results in victory over another Trainer and his Hitmonlee. Meanwhile, Team Rocket agents Attila and Hun have arrived at a Team Rocket base to view the Miracle Crystal. This invention can store electric energy and attract it as well—including Electric-type Pokémon. Jimmy, still on his journey, visits a Pokémon Center and he runs into an old friend, Marina, in the middle of a video conversation with their mutual friend Vincent. Marina wants to be a Trainer and a star performer, but when Jimmy tells her that's impossible, Marina challenges him to a 2-on-2 battle!
For the first round, Marina uses her Jigglypuff and Jimmy goes with his Beedrill. Jigglypuff's dance training does come in useful, but Beedrill wins the round. Next it's Marina's Croconaw against Jimmy's Typhlosion, but a strange lightning storm interrupts the battle. Marina's Misdreavus flies towards the storm, so she and Jimmy give chase. They catch up with Misdreavus at the source of the storm: Team Rocket's Miracle Crystal! Attila and Hun used it to stun all the Electric Pokémon drawn by its energy, and now they're just scooping up the stunned Pokémon.
Before Jimmy and Marina can stop them, another blast of lightning signals the presence of a powerful Pokémon nearby. The Legendary Raikou appears on a nearby peak, and it's angry! To protect the wild Pokémon, it attacks Attila and Hun, but the Team Rocket agents don't even blink. Every bolt of Raikou's lightning is simply absorbed by the Miracle Crystal, and the Crystal turns that energy back on Raikou with enough power to stun it. Now Attila is ready to capture it, but Jimmy confronts Team Rocket and tells them to leave Raikou alone—or else!