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.

Trey and Johnny disobey orders and attempt to rescue Trey's parents, who were inside an aerial clinic that crashed at a penal colony.

On their way back to Mauville City, Ash and friends travel through the Valley of Steel, home of many different kinds of Steel Pokémon and a potential shortcut to Mauville City and then Petalburg City. On their way through, they come across a Torkoal being attacked by several Steel Pokémon. After using Pikachu to scare the Pokémon away, the Fire-type hears a noise, also scaring it off. Later, having reunited with Torkoal, Ash and friends become determined to help Torkoal defeat the Steelix that lords over the valley. Will they succeed in cutting through the valley unharmed or will the angry Steel-type block their way?

May's Combusken manages to control the Fire Spin attack it launched. Through luck, May enters the next round with Kelly and fights Josaphine. In the final round, Kelly battles May, who has a tactic to overcome Grumpig's psychic powers. Just as Grumpig and Combusken are to fall down, May makes an honorable gesture. Meanwhile, Ash misses the contest to help his Swellow learn Aerial Ace.