Jackson panics, as Marina has been captured by Team Rocket. Jimmy shouts at Jackson to calm himself down, first. Jackson does so, but starts panicking again. Eusine, however, believes Team Rocket will do something nasty at Marina. Jimmy demands to do some action, quickly. Eusine calms him down, for that is the rule for rescue operations, though Jackson is still panicking. Jimmy has an idea and has Jackson call Marina through the Pokégear. Marina receives the call, but suddenly Attila takes the device and pushes Marina away. Attila grabs Little Miss, though Marina calls her in the Poké Ball. Jackson clarifies to Attila they will find them and defeat them properly. Attila shouts on the Pokégear, causing Jackson to faint, and logs off by smashing the device. Hun turns to Marina, preparing to intimidate her.
Eusine proposes to take the Pokégear, which will allow them to find the location where Marina called from. Elsewhere, Attila activates the crystal, ready to summon Raikou once more. Attila launches a signal to summon the black clouds, which terrifies Marina, who is tied up. Raikou, however, watches the clouds gathering. Jimmy, Jackson and Eusine take a car and also see the dark clouds. Attila detects the signal, but it is a Beedrill, who finds Marina and goes back. Eusine, Jimmy and Jackson arrive, whom Hun and Attila were expecting to be here. Seeing Marina tied up, Jackson becomes furious and is held by Jimmy, who orders him to calm down. They demand Marina and Raikou freed, but Eusine notices Raikou is not here, for they still have the crystal activated. Jimmy is certain Raikou will not come back, but Hun and Attila doubt him, for it is only a matter of time when Raikou comes here.
A thunder strikes the crystal, which emits electricity and strikes everything around. Attila tries to find Raikou, but another thunder strikes the crystal. Eusine deduces Raikou has re-gained its strength, allowing it to strike from a safe distance. A lightning strikes, knocking Marina down, but is rescued by Jimmy's Beedrill. Attila sends Skarmory, who uses Steel Wing, knocking Marina off Beedrill. Jackson trips over, causing Marina to fall on him. Jimmy comes to Marina, who thanks him for the rescue, as Jimmy unties her ropes. However, Jackson reminds them he cushioned Marina's fall. Hun sends Steelix, who uses Iron Tail, but Raikou appears and attacks Steelix. Jimmy and Marina ask Raikou to leave, as they can't protect it. Raikou, however, dodges the crystal's electricity and jumps, smashing Attila's machine, which causes the crystal to be unoperable. Skarmory uses Sky Attack, though Raikou pulls the machine's wires, causing the machine to explode and hit Skarmory.
With the machine exploded, the crystal does not function anymore. Eusine is fascinated, as Raikou was winning the battle from afar, yet it came close when it didn't had to. Jimmy believes Raikou wanted to protect them, since it had seen them as friends in need. Eusine wonders why Team Rocket has not retreated, since their plan is ruined. Raikou strikes with Thunder to attack Team Rocket, but the attack redirects onto the crystal. Hun and Attila explain the crystal is still active and has converted into an "auto-destruct" mode, causing it to sap Raikou's electricity from its own body. Jimmy orders Raikou to run, but Hun claims there is no way Raikou can flee, since it is tied to the crystal. Raikou is being binded, its electricity being absorbed, while Hun claims they rely on science and will triumph today as Hun and Attila will become legends.
Jimmy sends Typhlosion, along with Marina's Little Miss and Jackson's Meganium. Typhlosion uses Flamethrower, but the crystal protects itself with a shield. Jimmy claims they have to work together, but Eusine warns them that will cause a blast, which will destroy Raikou as well. Attila and Hun suggest not to overthink it, since they have no means to save Raikou. Eusine thinks there is a way: to open the crystal's field, take out Raikou and run before the crystal explodes, else nobody will come out alive. Jimmy has doubts, but Typhlosion is confident in winning over this crisis. Typhlosion, Meganium and Little Miss charge to free Raikou. Attila has Skarmory use Sky Attack, but is stopped by Typhlosion. Steelix uses Rock Throw, which hits Misdreavus and Little Miss. Eusine sends Alakazam, who uses Psybeam, which distracts Steelix.
Typhlosion uses Flame Wheel and Meganium Light Screen, hitting the crystal's field. Attila sends Muk, who uses Sludge Bomb on Meganium. Little Miss uses Psybeam on Muk, but gets hit by Skarmory, who dodges Alakazam's Psybeam. The crystal starts malfunctioning, so Eusine hopes Raikou endures a little longer to let the crystal's forcefield to disappear. Steelix uses Crunch, but misses its target. Attila asks the Pokémon will they rescue Raikou or their own trainers, but Jimmy and Jackson ask Typhlosion and Meganium to keep pressuring the field. Steelix goes to use Iron Tail, but is hit by Alakazam's Psybeam. Muk uses Sludge Bomb on Meganium and Skarmory attacks Typhlosion with Fury Attack. Steelix uses Iron Tail, attacking Little Miss and Alakazam, then goes after Jimmy, who is on the edge of a cliff. Steelix goes to use Crunch, but Jimmy taunts Steelix, claiming "it can't crunch a potato chip". Steelix strikes, but hits the ground, for Beedrill saves Jimmy. Steelix, however, damages the cliff and sinks down, into the river.
Attila and Hun are annoyed, so Skarmory and Muk go to finish off the "brats". However, they are attacked by Alakazam and Little Miss' Psybeam. Typhlosion and Meganium push the field and are about to destroy it. Steelix comes back and goes to use Crunch, but Jimmy, Marina and Jackson stand in its path. Raikou emits electricity, which pierces the field and hits Steelix. Raikou is freed, shocking Hun and Attila, since that was the top technology that was designed. Since the plan has failed, Hun and Attila retreat off. Raikou uses Thunder, crushing the crystal into pieces. Jimmy, Marina and Jackson thank Raikou for saving them. Raikou looks them and leaps off into the wilderness. Jimmy promises never to forget Raikou, and he and his friends cheer for the victory today.
- This is the only movie-length anime special that hasn't aired in Finland.
- Attila incorrectly refers to multiple Caterpie as Caterpies.
- Raikou's electric attacks worked on Steelix, even though Steelix is part Ground.
- In the Japanese dub, Hun tells Steelix to use Crunch. In the English dub, Hun tells Steelix to use Bite, a move it can't learn.
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