The movie starts off with a Pokémon battle. The battle is with Jimmy and another trainer. The trainer sends out his Hitmonlee and Jimmy sends out Typhlosion. Hitmonlee uses Jump Kick but Typhlosion blocks the attack by catching Hitmonlee's leg. Hitmonlee uses Rolling Kick with its other leg and it hits Typhlosion in the face. However, Typhlosion recovers from the attack which surprises the trainer. Hitmonlee uses Mega Kick but Typhlosion uses Flamethrower which knocks Hitmonlee out. Jimmy and Typhlosion "hi paw" each other and the audience claps. Jimmy then shakes hands with the trainer saying that he fought well.
The narrator talks a bit about Jimmy's background. Then the narrator tells us about Raikou.
A Team Rocket helicopter is flying above. The doors to their base open and the platform rises up so that they can land. They land on the platform and the doors close. Two people step out of the helicopter. Their names are Hon and Attilla. Their leader shows them a crystal that can control electricity. He shows Hon and Attilla a demonstration of the machine. The crystal starts to power up and then a bunch of metal rods come out of the walls. The rods fire electricity at the ground but it gets redirected towards the crystal which absorbs all the electricity. Their leader explains to them how the crystal works and what it does. They plan to use the crystal to capture Raikou.
Jimmy is walking on the path. He checks his PokeGear for the nearest Pokémon Center and he finds one that's close by. He walks in the Pokémon Center and he has his Pokémon healed. Nurse Joy tells Jimmy that the next town is far away and so he should stay for awhile. Jimmy is now grooming his Typhlosion with a brush and he tells it that he is very proud of it. Suddenly, Jimmy hears a voice. He gets up and he sees Marina talking on the phone. Marina's Misdreavus stares at Jimmy as he approaches Marina. Jimmy sees Marina talking to Vincent when he gets close enough. Then Vincent notices Jimmy and Marina turns around. Marina says hi to Jimmy and Jimmy gets red all over his face. Marina asks Jimmy if the Typhlosion is the Cyndaquil that he got from Professor Elm. Marina tells Vincent that she's got to go and then Vincent asks to speak to Jimmy. Vincent tells Jimmy that Marina is his girlfriend and he tells Jimmy that he knows that he likes her. Jimmy doesn't admit it and he hangs up.
Jimmy opens up a can of pop and him and Marina talk for awhile. Marina thinks that she should get Jimmy's PokeGear number so that they can stay in touch. Marina asks if Jimmy missed her but Jimmy wants to get off the subject. Marina tells Jimmy that she's changed a bit but Jimmy doesn't think so. Marina then tells Jimmy that she wants to be a rock star and she wants to sing a song that she wrote but Jimmy doesn't want to listen to it. Marina thinks that Jimmy likes her but Jimmy doesn't confess. Typhlosion smiles at Jimmy with a funny look and Marina thinks that it's cute. Jimmy wants to change the subject and she talks about training. She tells Jimmy that she wants to make people happy. Marina wants to be a great trainer just like Lance and she shows Jimmy her book of pictures. Jimmy doesn't think that being a rock star and Pokémon battles are the same and so he battles Marina.
They have their Pokémon battle outside. The battle is a 2-on-2 battle. Marina uses a little of performance movements and then she sends out Jigglypuff. Jimmy sends out his Beedrill. Jigglypuff starts off with a Sing attack but Jimmy tells Beedrill to use Agility. Marina exclaims that Beedrill should be asleep but Jimmy tells her that Beedrill's wings prevents it from going to sleep. Beedrill then uses Twinneedle but Jigglypuff dodges the attack by lifting off the ground. Jimmy orders Beedrill to go after it but Jigglypuff manages to dodge all of the Twinneedle attacks. Finally, Beedrill uses Pin Missile. Jigglypuff loses its air and it faints. Marina calls back her Jigglypuff and sends out Croconaw. Jimmy calls back Beedrill and he sends out his Typhlosion. Marina tells Jimmy that a water type vs a fire type is good but Jimmy likes challenges.
Suddenly, a few dark clouds approaches the area. Marina thinks that this will be a quick battle, so she orders Croconaw to use Water Gun. Croconaw uses the attack but Typhlosion withstands it. Typhlosion uses Quick Attack but just before it can hit Croconaw, a strike of lightning crashes down. Another flash of lightning appears and the Pokémon run away. Jimmy calls back Typhlosion and Marina calls back Croconaw. Just before Marina can bring back Misdreavus in its Pokéball, Misdreavus is gone. So they decide to go after Misdreavus.
Attilla sees that electric Pokémon are coming from many directions. The two Team Rocket members decide to hurt the Pokémon. The electric Pokémon arrive at the scene. The machine that Attilla's in grabs the Pokémon with its claws. Raichu uses a Thundershock at the machine but the electricity gets redirected towards the crystal. The crystal sends out a powerful blast which hurts the Pokémon even more. Misdreavus looks at the Team Rocket people hurting the Pokémon. Marina gets Misdreavus and Jimmy sees the people taking the electric Pokémon. Attilla holds the Pokémon up high with the machine's claws. Marina doesn't like this and they want to help.
Suddenly, a flash of lightning appears and a dark yellow cloud surrounds the top of a hill. The radar tells Attilla that it's Raikou. A great big flash of lightning surrounds the hill and Raikou appears. Jimmy looks up Raikou in his Pokédex. Raikou roars and jumps down the hill. It tells the Pokémon to run away and then it breaks the claws to the machine. Attilla fires more claws at Raikou but Raikou dodges them all. Raikou jumps into the air and fires a blast of electricity at them. However, the electricity gets redirected to the crystal. Raikou fires another blast of electricity at the crystal but nothing happens. The purple shield that surrounds the crystal gets bigger. Raikou fires more electricity at the shield but it bounces off and hurts Raikou. Raikou fires another blast at the crystal but the crystal reflects it back at Raikou. After a few more shocks Raikou falls to the ground.
Suddenly, Jimmy comes out and tells Team Rocket to leave Raikou alone. Team Rocket tells Jimmy to go home but Jimmy refuses to leave. He sends out his Typhlosion for battle. Attilla sends out Skarmory and Hon sends out Steelix. Typhlosion uses Flamethrower but Steelix blocks it off with Sandstorm. The Sandstorm starts to weaken Typhlosion but Jimmy tells his Pokémon to not give up. Attilla then commands his Skarmory to use Steel Wing. Skarmory uses the attack and Typhlosion falls to the ground. Now that the battle is over, Hon and Attilla continue to capture Raikou. Suddenly, Marina has her Misdreavus use Perish Song. While the Pokémon slowly begin to faint, Attilla continues to get Raikou. Jimmy sends out Beedrill and it uses Pin Missile to destroy the claws. Team Rocket's Pokémon faint and they plan to retreat. Their machine shoots out smoke and when the smoke clears, Team Rocket is gone.
Weakened from the Perish Song, Misdreavus falls from the air and Marina catches it and tells Misdreavus that it will be okay. Raikou gets back up on its feet and starts to walk away. Jimmy runs after it but Raikou shoots a Thundershock at Jimmy. Jimmy gets back up and starts to go after it but Raikou shoots another Thundershock at him. Raikou and Jimmy stare at each other and then Jimmy takes one step foward. Raikou shoots some more electricity at Jimmy but a Flamethrower from Typhlosion saves Jimmy. Raikou and Typhlosion sends another attack at each other. Jimmy tells Typhlosion to stop because Raikou doesn't understand them and thinks that they are going to hurt it. Jimmy gets up and tells Raikou to trust him. He walks a few steps foward. Raikou shoots another shock of electricity at Jimmy but Jimmy doesn't move. Raikou falls down leaving Jimmy to take care of it.
At the Pokémon Center, Marina is talking to Vincent. Marina plans to sing Raikou a song and Vincent agrees. Then Vincent tells Marina to release Raikou right away once it has recovered. A group of people stand outside the room where Raikou is because they want to see the Pokémon for themselves. Jimmy is watching Raikou in a room. Raikou has a few wires hooked up to it. Raikou observes the room that it is in and then it starts to hit the walls. Nurse Joy tells Raikou that no one will hurt it. Raikou just stares at Jimmy.
Hon and Attilla continue to fix up their machine. Hon tells Attilla that Raikou had a lot of energy still left and that it could still fight. Attilla gets mad by this and tells Hon that they will have to hit it harder next time. At the Pokémon Center, Raikou is sleeping. Jimmy and Nurse Joy continue to watch it when Marina tells Jimmy to take a break. Marina gives Jimmy a drink and she tells him to lighten up. Jimmy tells Marina that Raikou has been sleeping and that Nurse Joy has been giving Raikou more energy. A man comes rushing in and stares at Raikou. Marina thinks that the man is cute and asks for his name. Another man named Kuto comes in and he says hi to Eugine. Kuto and Eugine introduce themselves to Jimmy and Marina. Marina is all over Eugine but Eugine tells her to not touch the cape. It's night now and Eugine tells Jimmy a little bit about Raikou. Eugine tells them that men have always tried to capture Raikou and Kuto adds in that Raikou has never trusted humans before. Marina tells Jimmy to be careful next time because Jimmy could've been hurt back there. Jimmy thinks that Raikou can trust him and Marina smiles. Officer Jenny tells them that the men that tried to capture Raikou were from Team Rocket. If Team Rocket had Raikou, the whole world would be in danger. Raikou makes a promise to protect Raikou no matter what.
The next day, Raikou slowly opens its eyes and fires electricity out of its body which blows up the room that it was in. Jimmy jumps up and wonders what has happened. Jimmy introduces himself to Raikou. Raikou doesn't seem to be interested in Jimmy and it just fires more electricity at Jimmy. Everyone else enters the room and Jimmy tells them to stay back. Raikou fires another blast of electricity which blows up the wall. Raikou escapes from the Pokémon Center.
Dark clouds form from the sky. Jimmy tells Raikou that his strength is full recovered yet and that it could be in danger. Raikou doesn't listen to him and it rushes down to Team Rocket. Eugine appears in his red car and he tells Jimmy and Marina to come with him. He then tells Kuto to call for Officer Jenny. Team Rocket waits for Team Rocket. Suddenly, Raikou comes down and meets up with Team Rocket. Hon tells Raikou that they are the new masters of it. Raikou tries to destroy the crystal with electricity but the crystal just absorbs the blasts. Hon sends out her Steelix. Raikou fires electricity at Steelix but the blast just gets redirected at the crystal. Steelix starts off by digging underground. Then it bursts up where Raikou was standing. Raikou falls to the ground and then Eugine, Jimmy, and Marina come to the scene. Jimmy gets out of the car and tells them to stop. Jimmy tells them to battle fair but Hon tells him that being fair is not what they do. Jimmy gets mad at them and he tells them about battling. Raikou listens to Jimmy's speech.
Suddenly, Raikou jumps up. Attilla gets into his machine and the crystal fires electricity at Raikou. Raikou gets hit and falls to the ground. Jimmy takes out a Pokéball but all of a sudden Hon tells Steelix to use Rock Throw. The rocks are hurled at Jimmy and Marina. Suddenly, a blast of energy destroys the rocks. Jimmy and Marina look up. They see a boy and a Meganium. Marina thinks that it's Lance when the boy takes off his cape and reveals himself as Vincent. Vincent tells Meganium to use Solarbeam. Meganium fires the attack at Steelix but the attack does nothing to Steelix. Then Steelix hurls a Crunch at them but Vincent and Meganium escape just in time. Steelix uses Iron Tail on them and then it uses Rock Throw on Eugine. Meanwhile, Raikou is getting zapped with electricity. Then Team Rocket activates their capture bubble. The bubble hits Raikou but then Typhlosion uses Flamethrower on the bubble. Hon explains that the system is can only absorb electricity and nothing else. Marina tells Misdreavus to use Psybeam and Vincent tells Meganium to use Solarbeam. All three attacks are hitting the bubble. Steelix uses Iron Tail on the Pokémon but before the attack hits them, the bubble breaks. Attilla grabs Raikou and puts it in a storage room. They take off and fly away. Vincent exclaims that Marina isn't with them and Jimmy realizes that they must have Marina too.
Team Rocket is flying in the air and Hon asks her partner why she took Marina with them. Attilla looks at the screen and he sees Marina with Raikou. Marina bangs on the wall wanting to escape. Raikou wakes up and releases lots of electricity. The blast doesn't work because the walls are non-conductive meaning that electricity won't have any effect on them. Then Raikou tries to hit the walls hard but that doesn't destroy the walls either. Marina tries to calm down Raikou but Raikou doesn't listen to her. Then Raikou puts one foot on the ground which releases a bunch of wires. Marina runs to the wires and starts to pull on them. The wires break and the door opens. Marina and Raikou look down and they see that they are flying in the air. Attilla looks on his screen and he sees that the backdoor is open. Their vehicle starts to break down and they start to fly near some rocks. Marina tells Raikou to jump down. Suddenly, the door starts to close and Marina tells Raikou to hurry and escape. Raikou jumps and quickly glances at Marina. Then the doors close all the way, Hon tells Attilla to turn their plane around. Raikou lands and stares at the plane.
Vincent begins to freak out because Marina is captured. Jimmy tells Vincent to calm down but Vincent continues to cry. Jimmy asks Eugine for help. Eugine tells him that he has to remain calm even if Team Rocket has Marina. Vincent doesn't remain calm. All he does is scream and cry for Marina. Jimmy runs to Vincent and he tells him that they can try to call Marina through his PokeGear. Vincent takes out his PokeGear and calls Marina. Marina screams for help. Attilla has taken her PokeGear and Marina is jumping for it. Attilla pushes Marina to the ground. Misdreavus tries to attack Attilla but Attilla just grabs Misdreavus. Marina takes out a Pokéball and returns Misdreavus back. Vincent tells Attilla through the PokeGear to not mess with Marina. Attilla screams at Vincent to shut up and Vincent falls backwards. Jimmy takes the PokeGear from Vincent and he sees that the line has been disconnected. Attilla has smashed Marina's PokeGear and starts to walk towards her. Eugine tells Jimmy that they can find Marina's location by accessing the call log.
Team Rocket has landed and they start to set up the crystal so that they can capture Raikou. Then Attilla presses a button and the crystal activates. They launch a powerful beam of electricity and the dark clouds start to form. Marina has been tied up and a handkerchief has been put over her mouth. Raikou sees the clouds and wonders what it should do.
Eugine, Vincent and Jimmy are traveling in the car. Jimmy sees the clouds and Eugine tells them to hold on because he's going to go extra fast. Attilla detects something coming on the radar. Beedrill comes out and it stares at Marina. A red car pulls up and Jimmy, Eugine, and Vincent get out of it. Vincent demands to know where Marina is. Hon takes Marina and shows her to Vincent. Jimmy holds Vincent back and he tells Team Rocket to let Marina and Raikou go. Eugine tells them that Team Rocket doesn't have Raikou.
Suddenly, a jolt of electricity blasts the crystal. The crystal lets the electricity out and it damages anything that gets in its way. Another shock of electricity hits the crystal. Eugine says that Raikou has gotten stronger and that is bad. More electricity hits the crystal and the electricity hits the land near Team Rocket. Marina falls but Beedrill saves her. Attilla sends out Skarmory and he tells Skarmory to use Steel Wing. Skarmory flies towards Beedrill and hits it. Marina falls and Jimmy and Vincent come to the rescue. Vincent trips over a rock and falls. Marina falls right on Vincent's back. Jimmy asks if Marina is okay and Marina smiles at Jimmy. Vincent tells Marina that he saved her from falling to the ground and Marina thanks Vincent too. Hon sends out her Steelix. She orders Steelix to use Iron Tail. Before the attack hits them, Raikou comes out and hits Steelix back into the wall. Attilla makes the crystal shoot out more electricity but Raikou dodges all the blasts and it jumps straight for Attilla. Attilla jumps down from the machine and Raikou starts to destroy it.
Team Rocket starts to sweat and Attilla orders Skarmory to use Sky Attack. Skarmory charges straight for Raikou. Raikou jumps out of the way and just before Skarmory can hit Raikou, the machine blows up and Skarmory looses its control. Then the crystal powers down. Jimmy then says that Raikou came to save them and that it protects anyone who it thinks is a friend to it. Eugine is confused because Team Rocket hasn't fled from the battle yet even though they've lost. Raikou shoots a blast of electricity at Team Rocket but suddenly the crystal reactivates itself and the electricity is redirected at the crystal. Team Rocket explains to them that the crystal is still not destroyed. Hon tells them that the crystal is on auto-destruct. The crystal suddenly turns black. The crystal starts to pull at Raikou. Raikou tries to escape but the crystal doesn't let go. Team Rocket talks about their fame and then Jimmy sends out his Typhlosion. Then Marina and Vincent send out Misdreavus and Meganium. Typhlosion uses Flamethrower but the shield surrounding the crystal blocks it. Jimmy tells them that they should use their Pokémon's combined strength to destroy the shield. Eugine disagrees with them. He tells them that the blast could destroy Raikou. Eugine tells them his plan. He tells them that the Pokémon would have to break the shield, get Raikou, and escape as fast as they can. If they don't escape, all the Pokémon die. Typhlosion stares at Jimmy and decides to go with the plan.
The three Pokémon charge at the crystal. Attilla tells Skarmory to use Sky Attack. Typhlosion blocks Skarmory's attack and the other two Pokémon run on. Hon tells Steelix to use Rock Throw and the rocks almost hit Misdreavus and Meganium. Eugine sends out his Alakazam and it uses Psybeam on Steelix. Typhlosion uses Flame Wheel and Meganium uses Light Screen and then the two Pokémon push at the shield as hard as they can. Attilla sends out his Muk and tells it to use Sludge Bomb. Muk fires some sludge at Typhlosion and Meganium and then Misdreavus uses Psybeam on Muk. Skarmory knocks down Misdreavus. Alakazam fires a Psybeam at Skarmory but misses.
The two Pokémon continue to push at the shield with all of their might. Raikou then wakes up. Eugine says that if Raikou can stay awake, it can escape on its own and avoid the explosion. Hon orders a Crunch attack on Jimmy and the his friends. Jimmy and Vincent tell their Pokémon to try to save Raikou and to not worry about them. Steelix gets ready for an Iron Tail but Alakazam uses Psybeam on Steelix. Attilla orders Muk to use Sludge Bomb and for Skarmory to use Fury Attack. The attacks continue to hurt the Pokémon but Typhlosion and Meganium continue to endure themselves. Steelix uses another Iron Tail which knocks down Alakazam and Misdreavus.
Jimmy runs to the edge of the cliff and Steelix approaches him. Below the cliff is rushing water. Hon orders Steelix to use Crunch. Before Steelix can launch the attack, Jimmy mocks it by saying that it can't even crunch a potato. Steelix gets mad and steam fires out of its head. Steelix launches its whole body right to Jimmy. When Steelix gets close enough, Jimmy orders for Beedrill to get him. Beedrill saves Jimmy and Steelix misses and falls into the water. Attilla orders for Muk and Skarmory to finish the kids off but Alakazam and Misdreavus use Psybeam on both Pokémon. Typhlosion and Meganium continue trying to break the shield. Jimmy and Vincent cheer their Pokémon on.
Steelix pops out and aims a Crunch at Typhlosion and Meganium. Suddenly, Jimmy, Marina, and Vincent come forth to block their Pokémon from getting hurt. Raikou gets mad and with a final shot, it shoots a big blast of electricity at Steelix. Raikou escapes from the shield and the crystal begins to crack. Team Rocket retreats in their plane and they fly away.
Raikou fires one blast of electricity at the crystal. The crystal breaks into pieces. Jimmy, Marina, and Vincent thank Raikou for saving them. Raikou takes one last look at them and then it runs away. Jimmy says goodbye to Raikou and everyone puts their thumbs up.