The Legend of Thunder! (Part 2)

Plot
Jimmy has confronted Team Rocket agents Atilla and Hun who are about to capture Raikou with the help of the electricity-absorbing Miracle Crystal device. Atilla and Hun send out Skarmory and Steelix, catching Typhlosion in a Sandstorm attack and hitting it with Steel Wing. Marina sends in her Misdreavus for support and Jimmy sends his Beedrill to damage Atilla's capturing robot. Team Rocket finally retreats, leaving behind the injured Raikou. But even though Jimmy just wants to help, Raikou won't let anyone get close until it finally collapses and is taken to the Pokémon Center.

Even at the Pokémon Center, Raikou resents being in captivity. A strange man in a cape runs in to see Raikou for himself—his name is Eugene, and although he promises to help protect Raikou, he knows it's suspicious of people. In fact, the next morning, Raikou breaks out of the Center as soon as it wakes up and Eugene grabs Jimmy and Marina to follow it in his car. Team Rocket has set up another Miracle Crystal trap and Raikou is headed straight for it! Hun uses Steelix to provoke Raikou into using up even more electrical energy, but Jimmy, Marina and Eugene are soon on the scene.

Steelix turns its attacks on the Trainers, but Jimmy and Marina's friend Vincent appears and saves the day with his Meganium. The Crystal's absorption powers have exhausted Raikou, but Typhlosion, Meganium and Misdreavus can disrupt the Crystal's energy field if they all attack it at once. Despite their efforts, Atilla grabs Raikou and Team Rocket takes off. When the dust settles, Marina is missing as well! She was grabbed by accident and now she's with Raikou in the cargo hold of Team Rocket's ship. When Raikou's struggles dislodge a floor panel, Marina disrupts the ship's wiring and opens the cargo hold doors. Raikou escapes, but Marina is still inside the ship... and Team Rocket knows exactly what's going on!

Trivia

 * This special was later released on DVD for Japan, as well as Taiwan and mainland China.
 * By the time this aired dubbed, Eugene and Vincent had already been seen before, in For Ho-Oh The Bells Toll! and Love, Pokémon Style, respectively. In the episodes in question, they were named as Eusine and Jackson.
 * This special marks the first time that any characters based on game protagonists have appeared besides Ash, who is based on Red.
 * This special has the longest time between the original airings in Japanese and English, taking three and a half years to air dubbed.
 * This is the only movie-length anime special that hasn't aired in Finland.

Errors

 * In one scene, Hun commands Skarmory to use Fury Attack, but Skarmory is Attila's Pokémon.
 * When Raikou is put into the cargo hold, there is no sign of Marina, though she had been knocked down when Raikou collided with her after the bubble exploded.
 * Attila incorrectly refers to multiple Caterpie as Caterpies.
 * When Vincent's Meganium hits Steelix with SolarBeam, Hun implies that Grass types are ineffective against a Steel type like Steelix. This is not entirely true because Steelix's other type, Ground, is weak to Grass, and thus Steelix receives neutral damage from Grass-type attacks.
 * Raikou's electric attacks worked on Steelix, even though Steelix is part Ground. This, however, could be because of Raikou's sheer strength, similar to Pikachu. A similar situation occurs when Raikou tackles Steelix forcefully, sending it crashing into the cliff side.
 * In the Hindi dub, Misdreavus was once mispronounced as "Misdrees."

Dub edits

 * The dub of The Legend of Thunder is one of the most heavily edited episodes of Pokémon, most likely due to TV time constraints:
 * All of the music is replaced, besides the three seconds of Jigglypuff's song.
 * Hun was male in the Japanese version, but has a female voice in the dub.
 * The Trainer that Jimmy battles at the beginning had a name in Japanese, Shinji. The scene in which Shinji introduces himself and swaps Pokégear numbers with Jimmy is cut in the dub.