Our heroes have finally made it back to Pewter City, where Brock once again comes home to find the Pewter Gym looking stranger than ever. When he gets in the door, he discovers that his mom and dad are headed off on a free prize vacation, leaving the Gym in the care of three suspicious Gym remodelers who promised to make the Pewter Gym fashionable. His parents even took his Ludicolo to carry suitcases! Of course, it's all another Team Rocket scheme in disguise.
On a happier note, Brock meets Steelix, his evolved Onix. His siblings beg him to help them put the Gym back to normal. Team Rocket returns and realizes their new plan is full of twerps, but Team Rocket's Delibird drops off Poké Balls for them containing a Charizard and Aggron! With this firepower, they go in and challenge Brock to a battle—if they win, they decorate the Gym any way they want! Ash offers to help Brock out and it's time for a double battle.
Brock uses his Steelix, Ash uses his Donphan. Charizard is a tough opponent for Steelix to go up against and Aggron's no slouch, either! But Brock and Ash have teamwork on their side, unlike Team Rocket. Meowth sneaks off to steal Poké Balls while everyone is distracted, but Max blows its cover. Now Team Rocket's secret is out, and Brock's brother Forrest is outraged. Forrest, Brock, and Ash team up to beat Team Rocket. When Brock's parents come home, they get quite an earful from Brock, but family is family, after all. As for Team Rocket, they discover that all the bonuses they were getting were really meant for Butch and Cassidy!
En route to the Battle Pyramid, the group arrives at the Pewter Gym. A strange looks overcomes everyone and Brock explodes with the sight of the frightful remodeling of his beloved Gym. Brock is welcomed back with open arms by his siblings. After a few moments, all of his siblings form a single line. The oldest sibling instructs Brock that mother and father have left with the others confirming the statement. Brock places a video call to his parents who happen to be at an airport destined for a holiday. Brock is upset while his mother is in a joyous mood, acting as if everything is okay. As Brock displays his anger, his mother just ignores his comments and wishes him a goodbye as Ludicolo and Mime Jr. grant him the same parting. After she disconnects the call, two people dressed in airport staff attire and a Meowth arrive, handing Brock's father two tickets for a honeymoon. As the plane jets off into the sky, Team Rocket plot to capture the Pokémon of Pewter Gym now without a Gym Leader. Meowth goes into his usual illusions with Giovanni being pampered by Pewter Gym's former Pokémon.
Brock explores the newly renovated Gym further, noting the various streaks of colors plastered across the walls and floor. An adjacent door opens to the pathway and a Steelix grasps Brock's body and moves him closer. Brock realizes that his Onix evolved into Steelix while he was away. After a few seconds, Golem, Crobat and Geodude stampede into the arena, all pleased to see Brock's return. Brock turns to thank his younger sibling, Forrest, for his hard work and commitment in assisting the Pewter Gym.
Brock prepares a delectable lunch for his siblings and friends. Meanwhile, Team Rocket begins plotting their attack on Pewter Gym. After a few seconds, a Delibird descends from the air and delivers two Poké Balls to Jessie. Team Rocket escapes into a nearby field and call upon the two Pokémon; a meancing pair of Aggron and a Charizard. Now with two powerful Pokémon within their possession, Team Rocket arrive at Brock's residence and ring the doorbell. Everyone rushes to the door to see who the visitor is. Once Brock answers the door, Jessie and James are quick to forward a challenge to the ominous Pewter Gym. The kids hint that Team Rocket, or rather, their disguised selves were responsible for the Pewter Gym makeover.
A Double Battle gets underway as Ash and Brock call upon their Steelix and Donphan. Team Rocket release their Charizard and Aggron. Jessie doesn't hesitate to begin the battle as Charizard blazes forward with a Flamethrower striking Steelix directly. Donphan strikes Charizard with a Take Down and breaks through the ferocious stream of flames. Aggron launches forward with a Mega Punch colliding with Donphan and pushing him backwards. Steelix prepares to attack, but is knocked back by Charizard's Fire Spin attack. Aggron follows up with a Hyper Beam, tearing up the battlefield and finally coming to meet its target, Donphan, scoring a direct hit. As Donphan and Steelix recover, Ash and Brock reformulate their strategy. Donphan uses a Rollout attack which knocks Charizard off balance. Steelix follows up with an Iron Tail knocking Charizard backwards and then grasps onto it with Bind, constricting and restraining Charizard. Aggron launches a devastating Hyper Beam which hits Steelix directly and makes it release Charizard from its grasp. Charizard flies into the air and counterattacks with another Flamethrower as Steelix strategically uses its tail to uplift a rock to guard against the fire attack, following right away with a Dragon Breath, which pushes Charizard into a wall. Donphan charges at Charizard with Take Down, making another direct hit in a row. Aggron launches a Water Pulse attack striking Donphan knocking him backwards. Aggron continues to attack with another Water Pulse. The impending wave of water closes in on Donphan, but Steelix helps launch Donphan over the wake and strike Aggron.
Team Rocket's scheme is soon uncovered after Max spots Meowth escape off into the distance, and follows him into the Gym’s Pokémon storage area. As his hat falls off, Max realizes that Meowth is actually Meowth of Team Rocket. Jessie and James attempt to recover from the last round as Charizard launches another Fire Spin attack and manages to hit Aggron. Both Pokémon begin feuding and finally charge a corresponding Flamethrower and Hyper Beam which manage to collide and envelope Team Rocket. As the dust clears, Team Rocket's outfits are charred and soon crumble away revealing themselves to Ash and Brock. Meowth attempts to escape but Forrest manages to call upon his Geodude who Tackles Meowth, knocking him off course. Meowth drops the loot bag and a few Poké Balls roll out. Brock prepares to deal with the troublesome trio, but Forrest interrupts and has Geodude use Sandstorm on them. Aggron and Charizard go on the attack with Hyper Beam and Flamethrower while Steelix uplifts more rock to defend against the impending attacks. Geodude and Steelix blast forward, striking Charizard and Aggron with Mega Punch and Iron Tail. As Charizard and Aggron stumble from the attacks, everyone contributes to blast Team Rocket off with a fusion of attacks.
Brock's parents and Ludicolo finally return home, as Brock furiously orders a family discussion and reveals that Team Rocket were behind the Gym remodel scheme. At his friends' requests, Brock agrees to forgive his parents. Lola presents Brock with a wand-shaped souvenir, much to his frustration.
Meanwhile, Team Rocket hang from atop a tree as Delibird arrives to reclaim the Poké Balls it gave them earlier, explaining that they were supposed to go to rival Rocket duo Butch and Cassidy. Team Rocket attempts to reason with it, but are left feeling humiliated as Delibird flies off into the distance. The next day Brock and his friends leave for the Battle Pyramid, with Brock’s family wishing the group well on their journey.