After his journey with Ash and Dawn, Brock has returned home to Pewter City to take care of his siblings as well as studying towards gaining entry to a training school for Pokémon Doctors. Two of Brock's younger siblings come into his room and let him know that it is time for lunch. Brock gathers his siblings to the kitchen so that he can make them lunch, since their parents are away on yet another vacation. Meanwhile, at the Pewter Gym, Forrest calls out Steelix to battle a challenger, but the challenger refuses to battle him and says that she'll only battle with Brock or Flint. After gathering the rest of his siblings, Brock finishes the meal and they all get ready to eat. However, before they can begin, one of Brock's younger brothers runs into the kitchen and tells him to go to the Gym right away and inform him of the challenger's strange request. Brock and his siblings head to the Gym, where Forrest points Brock to the challenger. Brock quickly falls in love with the challenger and recognizes her as Nurse Joy, but his flirting is soon halted by Croagunk's Poison Jab. Nurse Joy removes her disguise and reveals that she used to run the Saffron City Pokémon Center, but is now a top-level agent of the Pokémon Inspection Agency. Forrest explains to his younger siblings that Gym Inspectors test Gym Leaders to ensure they will present a decent challenge to Trainers, and have the power the revoke the right to give out Badges or even shut down the Gym completely.
Brock explains to Inspector Joy that he gave the Gym Leader position over to Forrest, but she tells him that she did not receive any notification of the Gym Leader change, meaning that in her eyes, Brock is still the official Pewter Gym Leader. Inspector Joy agrees to battle Brock in order to assess his battling capabilities. Inspector Joy brings out her Chansey and Brock brings out Sudowoodo. Brock tells Sudowoodo to use Hammer Arm, but Chansey uses Minimize to avoid it. Chansey then uses Attract to infatuate Sudowoodo. With Sudowoodo unable to fight back, Chansey hits him with Double Slap. Seeing that Sudowoodo is getting weak, Brock issues a Flail, but Chansey counters with Egg Bomb, defeating Sudowoodo. Inspector Joy tells them that she will not be giving a good review based on the battle and that they should expect bad news. She informs them she will be remaining in the Pokémon Center until the next day and to come see her if they have any questions or comments.
As Brock and his siblings start to become very worried that the Gym may be closed down, Flint and Lola suddenly arrive back from their vacation with souvenir gifts for their children. They start talking about their trip and how great it was, but Brock interrupts them to tell them about the current crisis. He asks Flint about the Gym Leader change notification he had asked him to give to the PIA. Flint explains that while delivering the notification, he had found a beautiful rock and the notification had accidentally flown away in the wind while he had gone to pick it up. Brock is furious when he hears this, berating his father for not chasing after the notification. Flint and Lola tell Brock that the Gym closing down would be a good thing and that they would be able to change the Gym into a restaurant, but he immediately rejects the idea.
Brock heads to the Pokémon Center to speak to the Inspector Joy in her office. Brock asks her to give the Gym another chance and to test Forrest as a Gym Leader for the inspection. Inspector Joy says that she has to think it over. Just then, Pewter City's Nurse Joy comes into the office and says she has a problem and Brock tells her exactly how to solve it. Brock explains to Inspector Joy that he is studying to become a Pokémon Doctor, which is why he wanted to hand the Gym over to Forrest. Inspector Joy decides that she will test Forrest with a battle, and Brock goes home to tell everyone. At night, while everyone else is asleep, Brock notices that Forrest is not in his bed, and goes to find him at the Gym, where he is thinking about the upcoming battle. Brock gives Forrest some encouraging words, while their mom and dad look on from the stands and say that they are very proud of them.
The next day, Inspector Joy and Forrest prepare to battle, while Lola and Flint give their younger children Hawaiian outfits to wear for cheering on Forrest. Forrest brings out Rhyperior, while Inspector Joy brings out the Eon Pokémon Latias, shocking the entire family. Brock sees Inspector Joy's ownership of a Legendary Pokémon as a true sign of her being a top-level agent. Knowing that Latias is a Dragon/Psychic type, Forrest orders a Megahorn. Latias dodges the attack, but another Megahorn hits its mark. Rhyperior then uses Rock Wrecker, which Latias counters with Dragon Pulse before using Recover to heal herself. Forrest swears to protect the Pewter Gym and orders Rhyperior to use Horn Drill. Latias dodges behind some rocks before using Ice Beam, scoring a super effective hit on Rhyperior. As Latias prepares to use Ice Beam again, Forrest tells Rhyperior to use Dig, hiding underground and avoiding the attack. While Latias tries to locate it, Rhyperior resurfaces and uses Megahorn, scoring a direct hit. Inspector Joy tells Latias to use Recover again while Rhyperior once again hides underground. Latias is unable to locate Rhyperior, until it resurfaces again and strikes Latias with yet another Megahorn, earning cheers from Forrest's family, with Brock complimenting his hit-and-run strategy. Forrest prepares to finish the battle with another Megahorn, but Latias uses Dragon Pulse to stop it. While Rhyperior is able to deflect the attack, the resulting shockwave knocks some debris into the air and distracts it, allowing Inspector Joy to command a series of Steel Wings, which deal heavy damage on Rhyperior. One more Ice Beam from Latias, and Rhyperior has been defeated. Forrest is dismayed of having let his home Gym down.
Forrest and Brock go to attend Rhyperior, and Brock asks his Sudowoodo and Lola's Marill to get some Sitrus Berries so that they can heal it. Inspector Joy informs Forrest that she was impressed with the battle and that she will give a much better review than before, so they can expect the Gym to keep running, with Forrest as the official new Gym Leader. She also tells Brock that after witnessing his skills, she is certain he will be an excellent Pokémon Doctor. After Rhyperior is healed, Inspector Joy prepares to leave. Brock expresses his love to her, prompting Croagunk to Poison Jab him again. Everyone says their good-byes and Inspector Joy heads off.