Captain Spike is helping foil an attack from space bandits when he and Hoverrhycus crash land on Durus and lose communications with D.I.C.E. When Jet and Fortress F-99 go to the Gauron Space Prison, where they meet the Lady from Durus. She helps them find Captain Spike and they end up breaking her out, not knowing what will await them when they do.

Brock notices on his map there is a city nearby. Piplup goes in front of them to act as the leader. Suddenly, a Pokémon charges and the heroes duck, as the Pokémon might have hurt them, then it crashes some trees and departs away. Brock notices it was a Magnezone, while Dawn worries it goes towards the city. The heroes notice many Pokémon were hurt by Magnezone, so Brock gives them a berry and advises them to go to the Pokémon Center when they eat the berry. They notice Officer Jenny and talk to her (with Brock being attacked by Croagunk for flirting). Magnezone appears once more and wrecks a lot of stuff. As they follow it, a Metagross appears and wrecks stuff as well, but it also has a fight with Magnezone. To prevent this, Ash sends Monferno, who uses Flamethrower on Magnezone. The Magnezone and Metagross attack it. Monferno uses Mach Punch and gets hit by Metagross' Meteor Mash. Dawn sends Mamoswine to help out. Mamoswine uses Take Down and gets in collision by Magnezone. Mamoswine uses Hidden Power, but misses and gets hit by Magnezone. Brock sends Happiny, who stops Metagross. Jenny is pleased by Brock's work and he gets flattered, but also knocked out, as Metagross pushed Happiny on him. Metagross and Magnezone attack each other and go somewhere else. Team Rocket is about to have a meal and get blown away by Metagross and blasted off by Magnezone. Jenny never heard of those two in the town, so it is suspected something is on the mountain. To lure them, Brock believes some Electric-type moves used on the mountain should lure them. Pachirisu used Discharge and Pikachu used Thunderbolt, which lures Magnezone and Metagross, so they go towards the mountain. Suddenly, a trap is sprayed, as Team Rocket wants to get revenge on Magnezone and Metagross. They are explained that those two are fighting each other and Brock believes Meowth could talk to them to learn why are they fighting. Jessie whispers to James and Meowth if they could plan it, they could get both Metagross and Magnezone. Meowth talks to them, but he does not understand them. Suddenly, Metagross and Magnezone attack the balloon (causing Team Rocket to blast off) and depart. Pikachu and Pachirisu continue their luring, while Team Rocket plans to take Magnezone and Metagross by force. Suddenly, they encounter a mountain patroller named Crispin. Crispin explains that the basin has been the battle ground for the metal duo for some time, as it released magnetic energy. However, recently it was filled by water, so they took their battles elsewhere. They now know they need to drain the water out, so Team Rocket lends their help. Brock stops them, as he thinks they must know why the basin is filled, while Pachirisu and Pikachu keep Magnezone and Metagross close by. Crispin knows it has been raining, but there must be a source. Piplup detects a stream and upon following it, they encounter a boulder that blocks the path. Team Rocket comes and use their balloon to lift the boulder, but it is too heavy and they crash. Brock decides to take care of it, as he sends Croagunk. Using Brick Break, the boulder is smashed and Team Rocket swept away. They come to the basin and Team Rocket activates their pump to get the water out, but it is too slow. Brock thinks they could freeze it, so Dawn sends Buneary, who uses Ice Beam to freeze the water. Brock sends Happiny, who lifts the ice and tosses it in the valley. Pikachu and Pachirisu stop using Thunderbolt and Discharge, allowing Magnezone and Metagross battle in the basin. Team Rocket comes once more and Meowth attempts to persuade the duo to join Team Rocket. In response, Magnezone and Metagross blast them off. Seeing them battle, Ash sends Gible (who at first gnaws on a rock) to use Draco Meteor. The meteor fails to explode and Piplup is pushed in the pit and gets chased by the duo.

The Rangers fight Whiger and the other Phantom Beast Generals have given Camille their power and the Phoenix Spirit, and Dai Shi the Griffin Spirit, and made him their king. Whiger steals Casey's Tiger Spirit, and the Rangers are easily defeated without his help. When Whiger attacks again, Casey goes to Jungle Master Mode to help save the others and his martial arts students, powering the Claw Cannon with a student's Tiger Spirit. Whiger is defeated by the Megazords and flees.

As Ash plans on entering the League, he notices Pikachu being ill. Misty notices Togepi is like that as well, but does not feel it has fever. Brock thinks they have been walking in circles, while they also notice the Pokémon of the forest being ill as well. They hear a roar and upon coming to a lake, encounter a red Gyarados. It seems hurt, then uses Hydro Pump (which the heroes evade). Misty suggests to leave, but members of Team Rocket appear before them. Their leader sends a Fearow and Ash sends Totodile. Ash orders a Water Gun, but Totodile begins to feel ill. Fearow uses Drill Peck, but gets attacked by an Thunder Wave. A man and his Dragonite appear. The man orders the heroes to retreat into the forest. Ash calls Totodile back and retreats with Misty and Brock. Team Rocket goes after them, but Dragonite stops them, blowing a strong wind away. The Team Rocket leader promises he will get him next time. The man comes back and Ash is grateful. Pikachu is feeling better, and so is Togepi. The heroes tell they got lost on their way to Mahogany Town. Misty and Brock recognize the man being Lance, the Champion. Ash heard he is the undefeatable Dragonite trainer and introduces himself and so do Misty and Brock. Lance claims he came to uncover the truth about the red Gyarados and Team Rocket. The heroes decide to help out, but Lance refuses, since it is too dangerous. He points at a path and tells the heroes to go to Mahogany Town. Jessie, James and Meowth are tired and lost. They notice a strange farmhouse and think there is food inside, so go in it. The Team Rocket leader comes to Prof. Sebastian and reports the success. Sebastian is pleased, as they will have radiowaves that will affect all Pokémon. The leader knows they would craft a Pokémon army. Sebastian knows the equipment is inferior to record the radio-waves of red Gyarados, so the leader sees they need to lure it to the surface. A grunt reports intruders in the base, who are Jessie, James and Meowth. Jessie, James and Meowth notice a lot of Persian statues. Meowth has a feeling they are watched. James thinks there is nothing but statues and touches one. The statue glows, causing them to be captured behind metal bars. The leader comes and wants to know who they are. Jessie, James and Meowth chant their motto, while a grunt reports they have been demoted to rookies with 0% contributions. Jessie and James object on that. The leader sees they are hungry and thinks there is a job they can participate in. After a big meal, the leader orders Jessie, James and Meowth to come with him. They notice Prof. Sebastian, who reports the Project R will grant Team Rocket power. The leader gives them the order of capturing a Gyarados, surprising Jessie, James and Meowth. Sebastian tells them it lives at the bottom of the lake, while the leader lets them know they will be recorded in Team Rocket history if they succeed. The trio is interested in this work. Lance snuck into the base and put on a Team Rocket grunt's uniform. As the heroes continue on, Ash feels he has to go back and save Gyarados, who is in pain. Brock believes that Gyarados can be used to hurt other Pokémon if not stopped. With that argument, the heroes decide to go back. Team Rocket got on a spot at the lake, where Gyarados lives. James thinks they should use Poké Balls, but Meowth knows that it needs to be kept wild. Jessie knows this is for the boss, duty and country, so dives with James and Meowth. James dives further, but Jessie and Meowth think they need to oversee the operation. James believes they are scared, but Meowth and Jessie deny that. James thinks they shouldn't be afraid, while a pair of red eyes appear behind James. Jessie and Meowth are scared, and so is James, when he sees the red Gyarados. They come out of the water, while the leader orders the torpedo to be launched. The net is released, capturing the red Gyarados and the trio, then get electrocuted. The red Gyarados is pulled away, with the trio. The heroes observe, so Ash sends Totodile and Misty Poliwhirl, who go to help Gyarados. Totodile gnaws on the net, but ends up chewing Jessie's hair. The leader and Lance (disguised) notice the twerps, but Sebastian thinks they can test the radio-waves. These radio-waves affect Poliwhirl, Totodile (who are called back) and Meowth, shocking Jessie and James at his odd behavior. Pikachu and Togepi are affected, so Brock sees this radio-waves experiment causes them to be ill. The leader throws the rings, causing the twerps to be captured. With everything done, Jessie and James are pleased, while Sebastian lets the heroes know about Project R(evolution), which manipulates Pokémon, forcing them to evolve. Sebastian points at the red Gyarados, who is the proof of success. With its rage, the radio waves will force weak Pokémon to evolve into mighty ones. Jessie and James see that would allow Meowth to evolve into a Persian.