Brock is back in Pewter City after his adventures in Johto, but he finds his father Flint hiding at the edge of town. Flint warns him that something terrible has happened: Brock's mother Lola took over the Pewter Gym and turned it into a gaudy Water-type Gym! When Brock sees this, he's furious, but Flint is afraid to act and Lola won't listen. So Brock declares that Flint will battle Lola for the Gym—if Lola loses, the Gym goes back to the way it was. But if she wins, all of Brock's siblings will become Water-type Trainers!
With the Gym now a watery battlefield, Flint's Golem is at a disadvantage. Once Lola's Marill uses Surf, Golem sinks like a rock, and Lola's Blastoise has to fish it out of the water. When Flint starts to walk away, dejected, Lola reminisces about their first battle together. This rekindles their love, but Brock doesn't care. He's not even impressed when Flint and Lola try to patch things up by making the Pewter Gym a Rock-and-Water-type Gym. Brock's brother, Forrest, isn't happy either; he throws a fit and runs out of the house. Forrest doesn't want to be a Gym Leader now that the Pewter Gym isn't a Rock-type Gym, but Brock assures Forrest that he'll fix it.
The next morning, Brock insists on battling Lola for the fate of the Gym. Brock chooses Onix, and Lola chooses Mantine. Brock has Onix use Dig to drain all the water from the battlefield, but Mantine can still swoop through the air and use Water-type attacks. Still, the battle doesn't last long before Onix knocks out Mantine, and now the Gym is back to being a simple, no-frills Rock-type Gym. As for the family, they don't seem to mind. They give Brock a hearty send-off as he heads out to Hoenn, and Forrest promises to battle Brock the next time he returns!
Following his travels through the Johto region with Ash and Misty, Brock returns to his hometown of Pewter City. A mysterious man warns him to turn back, but Brock immediately recognizes his father Flint through the disguise and asks him what he is doing. Flint reminds Brock of the previous glory of the Pewter Gym, but then implies that something has happened, specifically his mother. Flint takes Brock to the Gym, which to his horror now features a hedge and flower garden. Brock demands to see the inside, but Flint admits Lola has the keys.
Brock arrives home where he is met by all nine of his siblings. His mother, Lola, puts up a Smeargle masterpiece on the wall, as she is becoming an art connoisseur. Brock recalls that the time he was there before she was studying astrological signs, and the time before that she was learning how to juggle yu-yu sticks. Brock comments that she is just being her usual bubbly self and that Flint may be overreacting, but Flint tells him to wait until he sees the inside of the Gym. While Lola is impressed with the Gym makeover, including a lake and painted walls, Brock is frustrated. The Pokémon come to meet Brock, and while Brock is impressed with Lola's Pokémon, he tells her that it is a Rock-type Gym and not an aquarium. Flint admits that he tried to stop Lola, however he gave up after Lola's Gyarados smashed the Gym’s rocks into pieces. Brock orders Flint to battle Lola to preserve the Gym’s heritage, Rock specialization. Lola agrees to it, on the condition that if she wins all of the other siblings have to become Water specialists. The siblings warn Brock that there is no way that Flint's Rock Pokémon can beat Lola's Water-type Pokémon. However, Brock remarks that Pikachu beat Onix despite the type disadvantage.
Brock calls for the one-on-one match to start, so Lola sends out Marill, while Flint sends out Golem. Golem starts out with an Earthquake. At first, it looks like it has worked, but then Marill turns things around with a Surf attack. This hits Golem, who starts drowning. Lola sends Blastoise to save it. As Brock uses a hairdryer to speed up the drying process, Forrest is impressed by Brock's knowledge of Pokémon. Lola tells Flint that he fought well, and they remember their first battle. Through this, they revive their love for each other. Brock is unimpressed, and still will not let the Gym become a Water Gym.
As Brock and his siblings prepare dinner, Flint and Lola remember the past in the Gym. Flint admits that he thought Lola was getting bored with him, but Lola tells him that he was the one thing that she never got bored of. Over dinner, Brock wants to talk about the Gym, but Flint and Lola are more interested in each other. They announce that the Gym will handle both types of Pokémon. It is Forrest that objects, telling them that they will turn the Gym into a laughing stock before running off. Brock learns that Forrest wants to become the Pewter Gym Leader when he grows up. Later, Brock finds Forrest sitting by a river. Forrest wants him to talk about the girls he has met, but Brock wants to talk about him. Forrest is now discouraged as the Gym is ruined and he will always lose to Water Pokémon. Brock vows that "tomorrow the Rock Pokémon will have their day."
The following morning, Flint shows Brock the new sign for the Gym, which Blastoise and Golem can't even hold up. Brock challenges Lola to a battle, stating that if he wins, she must take down her decorations, and the Water Pokémon will have to find another lake. Inside the Gym, Brock sends out Onix, while Lola calls out Mantine. Onix appears at a disadvantage, perched on a tiny island of rock in the middle of the lake. However, Onix leaps straight up, then dives down into its perch, starting out with Dig. With the rock destroyed, water floods into the new tunnel, which drains all of the water in the lake. Mantine flaps around, unable to move anywhere. Onix comes up underneath it which, while causing damage, allows Mantine to fly. It then launches a Bubble Beam, which Onix counters with Bind. Lola tries to get Mantine to use Confuse Ray, but it fails. However, another Bubble Beam does work. Onix lets go of Mantine, who goes into a third Bubble Beam, but Onix uses Slam, which makes Mantine faint. The Pewter Gym remains a Rock-only Gym, though Flint convinces the reluctant Brock to compromise and keep the color scheme.
Forrest congratulates Brock on his victory, and Brock assures him that he will be as good someday. On that note, he decides to give Onix, Geodude, and Crobat to Forrest to train with. Forrest promises to work to become a really strong Trainer. Later, Brock is standing outside in his Hoenn clothes, which Lola has made for him. Lola asks Brock if he has everything, and Brock confirms he has and will be taking Forretress with him to Hoenn, as it's not been long since it evolved and he would like to do some training with it. After saying goodbye to his family, Brock heads towards Hoenn to meet up with Ash once more.