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The special opens with a one-on-one pokémon battle. One trainer starts with his "number one", Hitmonlee. The other responds by sending out his "team leader", Typhlosion. Hitmonlee starts with a kick at Typhlosion, who catches Hitmonlee's leg. Hitmonlee frees itself by delivering a powerful kick to Typhlosion's head with its other leg. Hitmonlee's trainer seems to think the battle is over, but is proven wrong when Typhlosion shakes off the effects of the kick as if it were nothing. Hitmonlee is sent in for a High-Jump Kick. It leaps, and comes down right into Typhlosion's Flamethrower. Hitmonlee hits the ground unconscious. Typhlosion and its trainer exchange high-fives while Hitmonlee's trainer runs over to his fallen pokémon. The trainers shake hands and exchange compliments while Hitmonlee, now conscious again, speaks to Typhlosion. The Hitmonlee's trainer introduces himself as Shinji, from Kasado City on Gingan Tou (Silver Rock Island, featured in the Lugia mini-saga). The Typhlosion's trainer is Jimmy, from New Bark Town. They exchange pokégear numbers.
The narrator now begins speaking, introducing Jimmy as a trainer who raises, battles with, and grows strong along with his pokémon. In other words, he's perfectly normal. He then goes through a fairly standard introduction to the pokémon world, while various scenes involving pokémon are shown in the background. This is followed by the opening song.
Next, we see a brown VTOL aircraft with a red 'R' on the side flying low through what appears to be a canyon. A carefully camouflaged section of the ground opens to reveal a helipad. The VTOL craft lands, and is brought down into a massive underground facility. Out of the craft come two men in gray Team Rocket uniforms. They are greeted by a scientist who they address as Prof. Sebastian, and introduce themselves as Hun and Atilla. Sebastian has been waiting for them to arrive for a demonstration of his new "Crystal Field Generation System", or "Crystal System" for short. It involves a crystal which generates a field which is impenetrable to electrical energy. Furthermore, any electric discharge within the field will be redirected back to its source. Prior to forming the field, it can redirect nearby discharges into the crystal. Hun comments that electric pokémon will be helpless before the power of the Crystal System. Atilla says, "Yes, and after that, comes our part."
Cut to a scene of Jimmy approaching a pokémon center. In the center, Nurse Joy heals his pokémon, and invites him to rest there a while, since it's a long way to the next town. Jimmy accepts gratefully. We next see him brushing his Typhlosion. He is soon distracted by a familiar laugh coming from someone talking at one of the nearby videophones. It's a blue-haired girl, with a Misdreavus floating beside her. He watches her for a few seconds before the boy she's talking to notices and recognizes him. The girl turns to him and excitedly exclaims, "Jimmy!" Jimmy looks slightly embarrassed and replies "Yo, Marina."
Marina exclaims excitedly over his Typhlosion, asking whether it's the Cyndaquil he got from Professor Elm. Jimmy confirms that it is. She then turns back to the boy on the phone, Vincent, who asks to speak to Jimmy for a moment. Vincent beckons Jimmy close, then warns him not to try anything with Marina, as he wants her for his girlfriend. Jimmy replies, "Huh?" Vincent says, "I know you used to have a crush on her...". Jimmy blushes, denies everything, and hangs up abruptly.
Jimmy and Marina sit down, have a drink (soda, of course), and chat for a while. They discuss how they've changed (including an attempt at flirting by Marina), and discuss their plans for the future. Jimmy says something about becoming a great trainer. At the mention of great trainers, Marina says something about Lance. Jimmy says "Lance? As in, the Lance?"
She says "Of course!" and starts rambling on about the Great Lance, Dragon Trainer.... She even shows him her scrapbook full of pictures of Lance. She says her dream is to become an idol trainer, and finally be able to actually meet Lance. Jimmy is not impressed. Eventually, they challenge each other to a battle, to show off their pokémon.
The battle starts, but not before Marina does a little dance routine introducing herself and her Jigglypuff, Pink-chan. Jimmy is not impressed by this, thinking she needs to be a little more seriously. He sends out a Beedrill, and after a short conversation where Marina recognizes it as "that Weedle" (apparently one of Jimmy's early catches), the battle begins. Jigglypuff begins singing, and Jimmy orders Beedrill to use Agility. It works, as the buzzing of Beedrill's wings drowns out the song. Beedrill then goes in for a Twineedle attack, which Jigglypuff dodges by inflating and floating up. Beedrill tries a few more hits, not hitting even once. Eventually, Jimmy orders a Pin Missile attack. Jigglypuff can't hold out for long against such a barrage. It is forced to release its breath, which sends it flying off. Marina recalls it. Jimmy asks if she's giving up already. She says "of course not," and pulls out another pokéball.
After Jimmy asks her to please not dance again, she sends out a Croconaw, Wani-wani, which had been the Totodile she received from Professor Elm. Jimmy recalls Beedrill, and sends out Typhlosion. Marina thinks the type advantage will make this easy, and orders Croconaw to use Water Gun. Meanwhile, dark clouds are gathering in the sky. Croconaw's Water Gun scores a direct hit, but Typhlosion seems to hardly feel it. Jimmy orders a Quick Attack, which is about to hit when lightning suddenly strikes right in the middle of the battlefield. After checking to make sure everyone's all right, he says they'd better get back to the pokémon center. He and Marina start running, but their pokémon run the other way, towards the center of the storm. They manage to recall Croconaw and Typhlosion, but Marina's Misdreavus, Muu-chan, vanishes into the forest before it can be recalled. They follow it.
We now see the Crystal System, activated, in front of a large mecha. Atilla is in the mecha, looking at a computer display, while Hun is nearby with another computer, reporting on the system. Dozens of electric pokémon from the area are gathering around the Crystal System. Atilla uses the mecha to grab several of the pokémon. A Raichu tries to attack the mecha, but just before hitting, its thunderbolt turns away from the mecha and is absorbed by the Crystal System. It is then released outwards, striking the Raichu and many other pokémon. A particularly dark, lightning-filled cloud vortex approaches. This is where Jimmy and Marina finally catch up with Misdreavus. Marina scolds it, but they then notice the mecha grabbing pokémon. Jimmy is about to step out and do something, when lightning strikes a nearby hill from the cloud vortex. A roar resounds, and more lightning flashes. A new symbol appears on Atilla's display, much brighter than any of the ones that were there before. Atilla exclaims, "This has to be it!". Hun's comment is more reserved, a simple "It has come?"
A massive bolt of lightning strikes the hill. When it fades away, a large pokémon is there, yellow with black stripes, with what looks like a mask for a face. At Marina's prompting, Jimmy pulls out his pokédex to identify it. "Raikou, the Thunder Pokémon. Said to be a legendary pokémon, details are unknown."
Raikou roars, and comes charging towards the group. It jumps down among the gathered electric types, growls briefly, and all the pokémon start running away. It then charges the mecha, biting through the arms holding the pokémon. Hun and Atilla do not seem worried, as their mecha sends out several more arms aimed at Raikou. Raikou dodges by leaping into the air, and releases a most impressive Thunder attack aimed at the mecha. As with the Raichu's Thunderbolt, the attack is redirected into the Crystal System. Now knowing where its greatest threat is, it sends its next attack directly at the Crystal System. That, of course, is exactly what Hun and Atilla wanted, as it gives the System enough power to generate its field around itself and Raikou. Raikou launches an attack at the field, and is struck by its own power. It then attacks the crystal, with the same result. Jimmy and Marina look on in horror as this continues, until Raikou collapses. Hun orders Atilla to capture Raikou. He is about to do so, when they are interrupted by a voice. "Stop! Let Raikou go!"
It's Jimmy. They refuse, of course, and Jimmy sends out Typhlosion. Hun and Atilla respond by sending out Steelix and and Skarmory respectively. Jimmy says, "Hold on, Raikou. I will save you, no matter what."
Typhlosion leads off with a Flamethrower, and Steelix responds with a Sandstorm. As Hun says, "Flamethrower can't get through the Rock-type technique Sandstorm." With Jimmy's encouragement, Typhlosion struggles to get through the Sandstorm, only to fall to a Steel Wing attack from Skarmory. Hun and Atilla now get back to their job of capturing Raikou, starting by using the Crystal System to shock it. Typhlosion struggles to get up, but fails. Marina reluctantly sends her Misdreavus up against the two Steel types. Hun tells Steelix to use Crunch, and things are not looking good for Misdreavus, when Marina orders it to use Perish Song. The song affects both Steel types, and they are seemingly unable to move as it damages them. Hun calls Perish Song "a really annoying technique", as Marina apologizes to Misdreavus for asking it to do this to itself. While the pokémon are busy fighting, Atilla is about to use the mecha to capture Raikou, when Jimmy sends out Beedrill. Its Pin Missile attack does serious damage to the mecha, and Hun has to jump out of the way of a falling arm fragment. Realizing they can't win under current conditions, the two retreat under the cover of a smokescreen from their mecha.
Jimmy sees Raikou lying on the ground, as Misdreavus collapses into Marina's arms. She thanks it, and tells it to rest for a while. Raikou stands up and starts walking away. Jimmy tells it to wait. It replies by hitting him with a thundershock. He is sent flying, and Marina runs over to him, asking if he's all right. He jumps up, and runs back towards Raikou, asking what it's doing. It replies with another thundershock, this time aimed at the ground in front of him. The two stare at each other for a while, then Jimmy takes one step forward. Raikou instantly launches a thundershock, which is intercepted by a flamethrower from behind Jimmy. There is an explosion caused by the two attacks, and Jimmy is knocked backwards. His Typhlosion steps in front of him. The two pokémon trade one more set of attacks, before Jimmy tells Typhlosion to stop. He then walks straight towards Raikou, saying "Raikou, we are not your enemies. All we want to do is help you." Raikou launches one more thundershock, which passes inches from Jimmy's head. He doesn't flinch. They look into each other's eyes for a few seconds, before Raikou collapses.
At the Pokémon Center, Marina is talking to Professor Elm. He says he'll be sending a friend over. Meanwhile, word has spread that Raikou is in the Center, causing a crowd to gather in the lobby. In the back of the Center, Jimmy is watching Raikou, who is in a room by itself, hooked up to a set of wires. It does not seem happy, but Nurse Joy reassures it that it is in a place of safety.
Elsewhere, Hun and Atilla are repairing their mecha and planning their next attack. Atilla thinks it will be easy, but Hun warns him that they have not yet seen Raikou using its full power. Atilla seems more worried about "that hero-kid".
That night, Jimmy is still watching Raikou, and still alone (or so he thinks), when he is startled by Marina handing him a drink. They discuss Raikou for a little while, then Jimmy thanks Marina. Thinking he's talking about the juice she just gave him, she says it's no big deal. "Not that. I meant having your Misdreavus use Perish Song to help me, even though it hurt itself," he replies. The discussion continues, including a little flirting by Marina, until the doors open, and a man comes in demanding to know where Raikou is. He seems quite obsessed with "Raikou, the legendary pokémon to match Suicune and Entei."
Marina shoves Jimmy out of her way as she goes up to the man and introduces herself, and asks his name. Instead of answering, he asks "Who are you guys?", and is answered by a voice from the door saying that they're the ones who brought Raikou in. The man recognizes the speaker as "Kudou", who says, "It's been a long time, hasn't it, Eusine". Behind Kudou is Officer Jenny. Jimmy asks her who these people are, and she assures him that they're not there to cause trouble. Kudou introduces himself, saying he was sent by Professor Elm. Eusine says "I'm Eusine. I'm studying the legendary pokémon of Johto." He looks down at Marina, who is busily examining him from every angle, and adds "Please don't study me."
Later, Eusine tells them the legend of Raikou, the guardian of electric pokémon. After some discussion of that, Jenny says that the people who were trying to capture it were almost certainly from Team Rocket. Jimmy swears that he will protect Raikou.
The next morning, Raikou wakes up. Finding itself still hooked up to the wires, it breaks free, and lets off an electric blast that smashes the window between it and Jimmy, who is sleeping on a bench outside its room. He tries to calm it down, but it fires a thunderbolt at him. As Joy, Eusine, Marina, and Kudou come running, Raikou blasts through the outside wall of the Center, and runs off towards where clouds just like the ones from the previous day are gathering. As Jimmy and Marina shout after it, Eusine pulls up in a rather expensive-looking car. He instructs Kudou to stay behind and let Professor Elm know what's going on.
We see Hun and Atilla, their mecha, and the Crystal System in front of a large flying transport. Raikou arrives. This time, it does not attack them, instead walking around the System apparently looking for a weak point. Hun sends out his Steelix, and tells Atilla to set the Crystal System to protect it. Raikou launches an attack on Steelix. The Thunderbolt is redirected to the Crystal System, and from there, back out at Raikou. Steelix Digs to attack Raikou from below. Raikou is sent flying, and hits the ground hard. Eusine's car pulls up just then, between Team Rocket and Raikou. Jimmy gets out, telling them to stop. Addressing Jimmy as "Hero-boy", Atilla tells him "It's a wild pokémon. You pokémon trainers capture wild pokémon, don't you?"
The two have a heated philosophical discussion about whether their actions are morally different. It comes to an end when Atilla threatens Jimmy with physical violence. Raikou jumps over Jimmy, heading for Team Rocket. Atilla uses the Crystal System to hit it with electric blasts. Jimmy is about to send out a pokémon to stop them, when Hun orders Steelix to use Rock Throw. A large rock heads straight for Marina and Jimmy, but is destroyed by an energy blast from behind. They look at their rescuer. It's a cloaked figure, standing behind a Meganium. Marina gets excited, thinking it's her beloved Lance. She is disappointed, as it turns out to be Vincent, come to rescue his beloved Marina.
Vincent has his Meganium use another Solar Beam against Steelix. The Grass-type attack is ineffective against the Steel type. They get out of the way just in time to avoid being Crunched by Steelix. An Iron Tail attack sends the three youngsters sprawling, and Eusine is unable to send out his pokémon before being hit by Rock Throw. While their enemies are thus distracted, the Rockets continue on their Raikou-capturing process. The crystal generates its field, which expands, approaching Raikou. When it touches, Raikou screams in pain. The field's expansion stops as a Flamethrower hits it. The field is incapable of absorbing or reflecting non-electric energy. Marina sends Misdreavus in to help with a Psybeam. Vincent has Meganium use a Solar Beam. In order to prevent damage to the Crystal System, the Rockets are forced to shut the field down. As they do so, Hun has Steelix use Smokescreen. Under this cover, they use the mecha to grab Raikou and throw it in the back of their transport. Before the smoke clears, the transport takes off. Jimmy and Eusine are upset that they failed to protect Raikou. Vincent is devastated when he notices that Marina is also missing.
In the transport, Hun notices that Raikou isn't the only thing shown on the screen monitoring the back of the transport. "The girl who was with Hero-Boy" is also in there, with her Misdreavus.
Marina is not happy to be in there. Neither is Raikou. It lets off an electric attack, which is absorbed into the ceiling with no damage. It then tries tackling the walls, which is equally ineffective, but its foot opens a panel on the floor, revealing a bunch of wires. Marina grabs two handfuls of wires and pulls, breaking them. The back door of the transport opens. She and Raikou run to the door, but stop when they notice that they're hundreds of feet up. In the cockpit, an alarm goes off. The Rockets activate a backup system to close the door.
Before the door starts closing, Marina tries to convince Raikou to leave. She knows that while she couldn't survive the drop, it could. It seems reluctant to leave. When the door starts closing, she tries to push it out. Just before the door closes too far, it jumps, leaving Marina behind. The Rockets, seeing this on their monitor, are decidedly unhappy. Raikou lands and watches as the transport flies out of sight.
Vincent is going absolutely insane over Marina's disappearance. He shouts at Jimmy for even thinking about Raikou at a time like this. Jimmy, meanwhile, wants to set out in Eusine's car to find them, but Eusine reminds him that without knowing approximately where they went, it would be futile. After this refusal, Eusine has to stop Jimmy from setting out on foot. Jimmy realizes that Vincent has Marina's Pokégear number, and that they may be able to locate her using that. They use Vincent's Pokégear to call her.
At the other end of the connection, Atilla is tormenting Marina by holding the Pokégear just out of her reach. When she gets too annoying in her attempts to retrieve it, he hits her, sending her sprawling. When her Misdreavus floats up to protect her, he grabs it, forcing her to recall it before it gets injured. Over the Pokégear, Jimmy and Vincent shout at Atilla, demanding that he bring back Marina, thus annoying him so much he crushes it in his hand. The connection is broken.
Eusine asks to borrow Vincent's Pokégear. He thinks that by using its communications log, he may be able to locate Marina.
The Rockets are setting up for yet another attempt. Marina, bound and gagged, watches from a ledge on a cliff as they unpack and activate the Crystal System. It fires a beam up into the air, causing dark clouds to form in the formerly clear sky. Not far away, Raikou looks at the new clouds and growls. Jimmy, Vincent, and Eusine also see them, and now know exactly where to go. Eusine steps on the accelerator.
While waiting for Raikou, Atilla notices something approaching on his monitor. He knows it can't be Raikou, because it doesn't show up as an electric type, but not until it buzzes out of the forest can he identify it as a Beedrill. It buzzes around, looking at things, and Marina recognizes it as Jimmy's. As it heads back the way it came, Hun also identifies it. Moments later, Eusine's car comes out of the woods and screeches to a halt. Vincent gets out, and demands to know where Marina is. When the Rockets show that they are holding her as a hostage, he has to be physically restrained from going after them. They have a discussion on whether or not Raikou will fall for their tricks a third time, which is cut short by a bolt of lightning from an unknown source striking the Crystal System. As before, the electricity is absorbed, then sent back out in all directions. Bolts destroy Eusine's car and strike Team Rocket's mecha. Everyone realizes, between dodging bolts of lightning, that Raikou has found a way to use the Crystal System to its own advantage. This is not very reassuring, as everyone is nearly hit several times, and an explosion sends Marina flying off the cliff.
Jimmy's Beedrill catches her shortly before she hits the ground. Atilla sends out his Skarmory, and tells it to use a Steel Wing attack on Beedrill. Jimmy orders Beedrill to drop Marina. She goes down, Beedrill goes up, and Skarmory passes between them. Jimmy and Vincent run to catch her, but Vincent trips. Marina lands hard on Vincent's back. Jimmy arrives, asks if she's all right, and unties her. Marina thanks him, and the two are looking into each others' eyes, when Vincent groans and says "Hello, don't forget me, I was the one who saved you with my own body." Marina thanks him, too.
The reunion is broken up when Hun sends out his Steelix and orders it to use Iron Tail on the trio. Before it can obey, it is tackled into the cliffside by Raikou, who has just shown up. Its attack pattern this time is quite different. It dodges the electric blasts sent at it by the Crystal System, and heads straight for the cockpit of the mecha, where Atilla is controlling the System. Atilla gets out just in time, and Raikou smashes the controls. While it continues its destruction, Atilla sends Skarmory in for a Sky Attack. Raikou finishes what it was doing and gets out, leaving Skarmory to be blasted as the mecha explodes. The field around the Crystal System fades out. Jimmy finally realizes why Raikou kept coming back: It is the guardian of electric pokémon, who are affected by the System. As long as the Rockets have the System, it will keep attacking them. And now that the Crystal System's controls are gone, there is nothing to stop it. It launches a thunderbolt at Hun and Atilla, who are standing by the remains of their mecha. The Rockets simply smirk.
The Thunderbolt approaches the Rockets... and is diverted into the Crystal System, just like before. Hun explains that without their controls, the System will simply proceed with its preprogrammed Raikou-capturing procedure. Jimmy-tachi are horrified. They notice that the Crystal seems to be sucking light in. Hun proudly announces that the Crystal System is now going into "Black Hole Mode". The crystal turns black, and Raikou can only look on in horror as its energy is sucked out of its body. In this mode, even if Raikou doesn't attack, the System can take its electrical energy. It also physically sucks Raikou closer, until it is pinned up against the System's field. Jimmy sends out Typhlosion, and has it use its Flamethrower against the Crystal System. The attack is stopped by the Field. Marina and Vincent send out their pokémon, and the three are about to use their combined attack again, when Eusine orders them to stop.
At this range, any attack aimed at the Field will likely also hit Raikou. The combined effect of the three attacks could have very serious effects on it in its current condition. The three ask whether there's anything they can do. Eusine says that there is, but he seems reluctant to say what. When pressed, he says "zero-range attacks".
Jimmy and the others think about what this would mean. Simply getting to the Field would be dangerous enough, given the opposition. And then, if they did get through, the effects when the Field went down could be deadly. The three are agonizing over whether they can ask their pokémon to do this, when Typhlosion makes its own decision. It boosts its flame to a higher level than ever before, roars, and charges. Meganium and Misdreavus follow. Their trainers are shocked for a second, but then take command. Hun orders Skarmory to use a Sky Attack, but Typhlosion actually catches it in mid-strike, while the other pokémon run by. Steelix uses Rock throw, which stops Meganium for a few moments, until Eusine sends out his Alakazam, which hits Steelix with a Psybeam. The pokémon run past it. Jimmy orders Typhlosion to use Flame Wheel, and Vincent has Meganium form a Light Screen. The two strike the Field, and press their attacks up against it. Atilla sends out a Muk, which uses Sludge Bomb to try to knock the two away from the Field before they can do much to it. Misdreavus stops Muk with a Psybeam, but is knocked away by a wing strike by Steelix, who is in turn hit by Alakazam's Psybeam. As the two pokémon continue to attack the Field, hoping thereby to damage or overload the Crystal System, Hun comes up with a new way to stop them. He orders Steelix to use Crunch - on the trainers. He then speaks to the pokémon, telling them that if they continue, their trainers could get killed.
As the dust clears from the Crunch attack, Jimmy and Vincent assure their pokémon that they will be all right, and tell them to just focus on what they're doing. Steelix is about to hit them with an Iron Tail attack, but is stopped by a Psybeam from Alakazam. Atilla orders his two pokémon to continue trying to stop Meganium and Typhlosion. Muk uses another Sludge Bomb, while Skarmory uses what I'm fairly sure is Faint Attack (literal translation: "foul play"). Steelix sends Alakazam flying with Iron Tail, then goes after Jimmy. It chases him to the edge of a cliff above a river. Jimmy's friends shout at him to run for it, but instead he looks Steelix in the face and delivers a deadly insult (calling the Haganeru, "Bakaneru"). As it gets steamed, and lunges down to smash him into the rock, he signals to Beedrill. With perfect timing, it swoops by and grabs him at the last second, carrying him away as Steelix hits the ground hard, sending the section of cliff edge it is on down into the river. Atilla orders his two pokémon to finish off Typhlosion and Meganium, but they are hit by twin Psybeams from Alakazam. It seems that Typhlosion and Meganium are about to finish, when Steelix bursts out of the ground. It is about to finish the two pokémon off with a Crunch attack, when it finds its way blocked by Jimmy, Marina, and Vincent, protecting their pokémon with their own lives.
Seeing this, Raikou exerts its full effort. It manages to pull its power away from the now apparently damaged crystal, and blasts Steelix with the most potent electric attack ever seen in the anime. Looking at Raikou, who is now surrounded by the aura of its power, the Rockets realize that with the crystal damaged, they cannot win. They retreat in their transport, abandoning the Crystal System. With the System now completely inactive, Raikou finishes it. An electric blast reduces the crystal to shards, and sets the rest of the system ablaze. Jimmy and the others watch Raikou leave. Jimmy calls after it, "Until we meet again!"
In the next scene, they leave the Pokémon Center, saying goodbye to Jenny, Joy, Eusine, and Kudou. Kudou tells them all, especially Jimmy, not to try to do the impossible too often. They set off, and the ending music starts playing. Where the trail splits, they part, thinking back to the day they left New Bark Town, and thinking how similar this parting is. Jimmy goes straight, and once he is gone, Vincent asks Marina to call him later, and she agrees. Vincent then leaves, and Marina looks after him for about half a second, before her gaze shifts to Jimmy. She watches him for a while, then sets off on her own road, with Misdreavus following. The credits roll.
Jimmy is walking through the woods when his Pokégear rings. It's Marina. Apparently, before leaving the Pokémon Center, she had gotten a new Pokégear, and got his number from Vincent. She offers to give him her number. He accepts in a fairly calm voice, but makes a "YES!" gesture as she gives it to him. The scene zooms out, the narrator sas a few final words, and the special ends.
Special Thanks to Murgatroyd for writing This
Legend Of Thunder
Raikou: Legend Of Thunder