Raikou was first lured by Team Rocket agents, Attila and Hun, using Team Rocket's Miracle Crystal, a device invented by Professor Sebastian. It freed the Electric-type Pokémon from the mecha the duo was using. With Raikou there, they turn on the crystal to protect themselves from Raikou's electric attacks. As Raikou was beat, Jimmy stepped in to prevent Team Rocket from harming Raikou even further.
After defeating Attila and Hun, Raikou was still injured and when Jimmy offered to help it, Raikou fired some electricity at him. With his Typhlosion protecting Jimmy from anymore electrical blasts, Raikou allowed Jimmy to help it recover. Raikou was taken to a Pokémon Center where it would recover. After Raikou was fully healed, it escaped the Pokémon Center and went after Attila and Hun again. The crystal once again proved to be a challenge for Raikou.
With Raikou once again weakened by the crystal, Attila used a capture bubble to absorb its electricity, but Typhlosion's, Little Miss's, and Meganium's attacks destroy it. However, this didn't stop Attila from taking Raikou as he successfully placed it in the cargo hold of the mecha. Unbeknownst to Attila, Marina was caught too. She was able to open the door of the cargo hold and Raikou managed to jump out before the door closed. Far from the crystal's activation, Raikou attacked it which caused destruction from the crystal's energy waves.
Despite the crystal being rendered useless, Team Rocket had a trick up their sleeve. With the control panel destroyed, the crystal became twice as powerful since it is running on auto-destruct. The crystal grabbed Raikou and trapped it inside a bubble. The group do their best with destroying the bubble as it proved to be a challenge for them unlike last time. Typhlosion and Meganium volunteer to drain the energy from the force field. Despite Attila and Hun stopping them from freeing Raikou, Raikou broke out in the nick of time to protect the group from Steelix's attack. Raikou then destroyed the crystal for good, and runs off with Jimmy and his friends waving goodbye to it.