With rumors of a Red Gyarados rampaging in the Lake of Rage, Lance of the Elite Four decides to investigate.
In Mahogany Town, Lance of the Elite Four and his Dragonite arrive at the local souvenir shop. Inside, Lance knocks on a wall two times and then has Dragonite use Fire Punch to crack the wall open. The wall breaks, revealing a secret passageway to an underground room. Lance and Dragonite go down a slide and arrive at a hallway that is part of Team Rocket's secret headquarters. While running down the hallway, Lance has a flashback of why he came to investigate the Team Rocket HQ. Earlier, at the Lake of Rage, he and Dragonite encountered a rampaging Red Gyarados, which fiercely attacked them. Concluding that it wasn't acting normally, Lance deduced it had been forced to evolve by a mysterious radio wave. He decided to find the source of this radio wave, which led him to the souvenir shop.
As the two keep running down the hallway, they accidentally trigger a security signal as the eyes of a Persian statue light up. The statue turns out to be a secret security camera which is monitored by a Team Rocket Grunt. The Grunt warns his fellow Grunts that their headquarters have been intruded. One of the Grunts recognizes the man on the security footage as Lance. The screen then switches to other security footage which shows that there is another intruder, which turns out to be Ethan. The Grunts decide to go stop them in their tracks and sound the alarm.
As Lance and Dragonite arrive at a bridge, their path is blocked by four Team Rocket Grunts. Lance remarks that he was right in thinking Team Rocket was behind this but also that he thought Team Rocket had been disbanded. In response, the Grunts smile and send out a Grimer, Magnemite, Raticate, Golbat, and Houndoom. Lance orders Dragonite to break through and it lets out a huge roar. The Grunts have their Pokémon attack simultaneously, but Dragonite fends off the attacks with no trouble at all. Dragonite easily defeats all the opposing Pokémon with a single Flamethrower and uses its tail to knock them off the bridge. The Grunts realize Lance and Dragonite are too powerful, and the Elite Four member and his Pokémon are now able to continue on their path.
Next, Dragonite knocks down an iron door and the Pokémon and its Trainer arrive in a control room. Lance runs over to a window and sees how multiple Electrode are attached to a large machine. The Ball Pokémon are forced to give off electricity to power the radio transmitter that emits the mysterious radio waves. As Lance watches, he hears a voice behind him. Petrel, a Team Rocket Executive, appears and concludes that Lance and Ethan have been working together, with Ethan being a diversion for Lance. Petrel sends out his Weezing and has it use Poison Gas. Lance orders Dragonite to do something and it simply walks through the poisonous gas clouds. Following this, Dragonite uses Thunderbolt, hitting both Weezing and Petrel and fainting the former. Lance tells Petrel that Team Rocket's operation is finished and orders him to leave. As Dragonite intimidates Petrel, Lance communicates with Ethan through his Pokégear and tells him that they're going to take down the source of the radio waves. In response, Ethan simply smiles.
Lance walks over to the Electrode and promises to free them. He has his Dragonite destroy the control panel and break open the window. After doing so, the generator is shut down and the Electrode are freed from the machines they were attached to. Lance tells the Electrode to escape and they happily bounce away from the generator. They gather in front of Petrel and shock him with Thunderbolt as revenge for what he did to them. Later, at dusk, Lance stands at the shore of the Lake of Rage. Seeing that the Red Gyarados has calmed down, he walks away as the Atrocious Pokémon dives back into the depths of the lake.