As the journey to Daybreak Town and Dawn’s next Pokémon Contest continues, our heroes are passing through the forest when they are suddenly attacked by a wild Magnezone! They later speak to Officer Jenny, who informs them that the wild Magnezone, as well as a wild Metagross, are attacking a nearby town, and no one seems to know why. Fearing for the town’s survival, Pikachu and Pachirisu start shooting Electric attacks into the sky in an attempt to lure the two wild Pokémon back up to the mountain.
Later on, Ash and friends run into a patrolman named Crispin, who tells the group that the two wild Pokémon always battle in a basin in the mountain. They battle there in order to release the magnetic charges that the mountain produces from time to time, but the basin has mysteriously been flooded. As they figure out how to remedy the situation, Team Rocket decides to get the two wild Pokémon to join them...with the help of some negotiating by Meowth. But their plan fails over and over, and they are sent blasting off again.
With the help of Buizel and Happiny, the water in the basin is frozen and then lifted up and into a deep crevasse. The basin is ready for Magnezone and Metagross to battle happily once again!
As Ash and his friends continue their journey to Sunyshore City, they narrowly miss being attacked by a wild Magnezone. They watch as the rampaging Pokémon heads towards a nearby town, and rush over to stop it. By the time they reach town, several Trainers are already trying to nurse their injured Pokémon. Brock offers them each some advice and an Oran Berry as the group continues to investigate. They are later informed by Officer Jenny that Magnezone — soon joined by a wild Metagross — has suddenly appeared and is wreaking havoc throughout the town. The group direct their Pokémon to stop the fighting, but the Magnezone and Metagross prove too powerful for Ash's Monferno, Dawn's Mamoswine, and the might of Brock's Happiny.
Later, Brock suggests that they lead the two Pokémon down the mountain with electricity to keep them from destroying the city. Pikachu and Pachirisu are up for the job, but before they reach their destination, Team Rocket interrupt. They want to get their revenge on the two battling Pokémon for disturbing them not once, but twice. Brock asks Meowth to talk to the two Pokémon to ask them why they are fighting, but even he can't understand the strange metal language. Team Rocket are sent blast off after a hit from Metagross. With no other options, Pikachu and Pachirisu use Thunderbolt and Discharge respectively and repeatedly in order to continue leading Magnezone and Metagross down the mountain.
The group meets up with Crispin, a local Pokémon Ranger. Crispin informs them that the two Pokémon normally battle with each other to release the magnetism that builds up in their bodies, due to the strong magnetic forces emitted from the mountains. Recently, however, their "battle arena", which is a deep crater has become filled with water. Ash, his friends, Officer Jenny, and Crispin realize they have to find out why the crater is full of water, and then find a way to drain it, so Magnezone and Metagross can battle in peace, away from the city.
They discover a boulder diverting a stream to the crater, and Team Rocket reappears to move the obstacle with their balloon. Unfortunately, the boulder is too heavy and their balloon ends up falling into the river. Brock then sends out his Croagunk, which uses Brick Break to break the rock, restoring the normal flow, taking Team Rocket with it. With the water no longer flowing to fill the basin, they can now drain it. Team Rocket returns and tries to help once again by using their pump to drain the crater.
Unfortunately, their pump's motor is weak, meaning that it would take too long to get the water out. Therefore, Brock suggests freezing the water. So Dawn sends out her Buneary to use Ice Beam on the crater. Unfortunately, since Team Rocket's pump hose was still in the water, they get frozen too. Brock then sends out Happiny to lift the ice out of the basin with Team Rocket as well. Despite Team Rocket's begging, Happiny throws the ice mass and them into the valley. With their battle area freed of water, Magnezone and Metagross can battle as much as they want, out of the way of the city.
Deep into battle, however, Team Rocket appears again and tries to appease both Pokémon by claiming they saved them both, not Ash nor his friends. This backfires, and an explosion launches Team Rocket into the sky, away from the crater. The battle continues, but then Ash sends his Gible for some practice. However its Draco Meteor fails once again, knocking Piplup into the crater below, where he is forced to dodge Magnezone's and Metagross's attacks.