The Hoenn League has ended and our friends must go their separate ways. Tyson and Morrison are off to new adventures; May and Max return to Petalburg while Ash and Brock head back to Kanto. Even Team Rocket goes back to headquarters and reports to a thoroughly unimpressed Giovanni. Butch and Cassidy show off their cool new jetpacks, so Team Rocket demands they get something cool too—and end up with pogo sticks.
Ash is now alone, Brock having headed home to Pewter City. In Viridian City, Ash encounters Scott, a flashy fellow who wants to talk about the Battle Frontier. But first Ash ends up challenging the new Viridian Gym Leader, a woman named Agatha. With typical confidence, Ash sends Pikachu to battle Agatha's Gengar and forgets that as a Ghost-type Pokémon, Pikachu won't be able to hit it with normal attacks.
Although Ash quickly adjusts his strategy and Pikachu does its best, it just can't beat Gengar. Still, Agatha is impressed that Ash at least showed some spirit. It's now that Ash learns Agatha is also one of the Elite Four, so it's great that Pikachu managed to last that long in the first place! Scott encourages Ash to try for the Battle Frontier, a series of seven challenges, but they're briefly interrupted by Team Rocket's latest short-lived Pikachu-snatching attempt.
Once Ash finally makes it back home, he finds Misty and her new Azurill waiting for him—and Professor Birch and Max show up as well! A memorable get-together is in the works...
With the Ever Grande Conference now over, Ash bids farewell to Morrison and Tyson before leaving Ever Grande City. Ash and his friends then head to Oldale Town to say their goodbyes before heading their separate ways. While preparing to eat lunch, May comments on how she and Max are going to miss Brock's cooking when they return to Petalburg City and wishes they could bring some of Brock's recipes with them. Ash asks if they will remember to say hello to Norman for him, and Max promises to do that as well as tell him that Ash should have won the Ever Grande Conference, much to Ash's embarrassment. Brock tells Ash that they should stop by to see Professor Birch in Littleroot Town. May and Max tell Ash that they will make sure to visit him in Pallet Town some time. Munchlax pops out of its Poké Ball and eats their lunch of rice balls, but Brock had prepared extras just in case. Before May and Max split off to return home to Petalburg City, the four friends say their goodbyes and tell each other to make sure to keep in touch.
Team Rocket returns to the Team Rocket headquarters to speak to Giovanni about their progress they made in the Hoenn region. They are reluctant to face him and are worried that he will be very upset with him, but go in anyway. Jessie and James say that they were the ones responsible for taking down Team Aqua and Team Magma, forcing them to disband. Giovanni does not believe them, but gives them a new assignment and says that it is their reward for their hard work. As they are leaving, Team Rocket comments that being convincing does pay off and reward them, revealing that Giovanni had assigned them to Antarctica, although none of them has ever heard of it. Just then, Butch and Cassidy run into Jessie and James with motorized scooters and yell at them to move out of the way. Jessie tells them that they were given a top-secret mission and tries to knock Cassidy over. Cassidy tells Jessie that Giovanni was just trying to get rid of them. They continue glaring and arguing with each other, until a Team Rocket Grunt runs up to Cassidy and Butch, saying that Professor Namba has a very important assignment for them, and they rush off. Stepping outside, the trio decides to start anew as a new and improved Team Rocket, only to then get laughed at by Butch and Cassidy, who fly off with her packs. The trio demands their own equipment from a nearby Grunt, but another Grunt then shows up, telling them that he's got their promised equipment for them. To the trio's embarrassment, however, their "equipment" turns out to be set of pogo sticks. They bounce away on them, but accidentally fall over.
May and Max arrive in their hometown of Petalburg City. Caroline greets them and tells them that Norman is out shopping at the moment. They go to see the Pokémon in the greenhouse and May brings out all of her Pokémon to play. Skitty falls asleep in a tree, Bulbasaur smells some flowers, and the other Pokémon run around and play. Meanwhile, Ash and Brock have reached a crossroads and split up to head to their respective hometowns. While stopping for a break a bit later, Ash spots a Poliwag and asks Max to come look at it, before remembering that he is all by himself now. On his way through Viridian City, Ash notices that the Viridian Gym has been rebuilt after it collapsed. A man introducing himself as Scott approaches him and asks if he is there to challenge the Gym Leader, but Ash tells him that he has already won the Earth Badge. Scott is impressed and tells Ash that he may be a good enough Trainer to challenge the Battle Frontier. However, before Scott can explain more, an older woman screams as she falls off of her bike nearby and Ash and Scott go to check on her. The woman introduces herself to be Agatha and tells Ash that she's been working as the new Viridian Gym Leader for several months now. She takes the two into the Gym, and Ash notices that it now looks significantly different than the last time he was there, all thanks to a new coat of paint. Agatha asks Scott how his search for a strong Trainer from the Seafoam Islands is going, but Scott says the information is confidential. Agatha asks Ash whether he is there to challenge the Gym and Ash explains that he has already won a Badge from the Gym. Scott suggests that Ash should battle Agatha just for fun, and she admits that she defeated the last two Trainers who had come to the Gym with ease and could use a little challenge. Ash mentions how he had just made it to the top eight at the Ever Grande Conference, impressing both Agatha and Scott. By Agatha's request, Scott agrees to act as a referee.
Ash calls out Pikachu, while Agatha chooses Gengar, whom Ash scans with his Pokédex. Pikachu starts out with Quick Attack, which simply phases through Gengar since it is a Ghost-type Pokémon. Agatha criticizes Ash for forgetting such a basic detail. Pikachu uses Thunderbolt as Gengar flattens its body to move under Pikachu and dodge the attack. Gengar uses Shadow Ball as Pikachu dodges. Pikachu then uses Iron Tail to hit Gengar, sending it to the ceiling. As Pikachu leaps in for another attack, Gengar uses Shadow Ball and hits Pikachu. Pikachu climbs over the Shadow Ball and prepares for another Iron Tail, but Gengar uses Double Team to completely surround Pikachu. Gengar starts charging for a Shadow Ball as Pikachu uses Thunderbolt to hit all the fakes and the real one. Despite being hot, Gengar is able to release the Shadow Ball, which Pikachu dodges before using Iron Tail to land another hit. Just before Pikachu is about to finish it off with Thunder, Gengar uses Hypnosis to stop the attack, before following up with Dream Eater to defeat Pikachu. Agatha compliments Ash of the good battle, and he admits to Agatha that he's not even nearly as strong as she is. Scott comments that Ash shouldn't expect to have beaten one of the Elite Four. While Ash expresses his surprise at Agatha's status, she explains that the official Gym Leader hasn't arrived yet, so she's just filling in for the time being.
Meanwhile, Team Rocket has been observing the battle and comment on how strong Pikachu really is. They decide to try to capture it and lower their balloon behind the Gym. In front of the Gym, Scott asks Ash if he is still interested in challenging the Battle Frontier and begins to explain how it works. He explains that there are seven Battle Frontier facilities spread out across Kanto that are run by Trainers known as Frontier Brains, who are like Gym Leaders but more powerful. Like Gym Leaders hand out Gym Badges, each of the Frontier Brains hands out a Frontier Symbol if defeated, and once six Symbols have been earned, the location of the secret seventh facility will be revealed. Ash decides to challenge the Battle Frontier and Team Rocket, having eavesdropped the entire conversation, decides to make it their next target. Team Rocket then grabs Pikachu with a mechanical grabber, before revealing themselves and reciting their brand-new motto. They try to get away, but Agatha's Golbat uses Air Cutter to cut the grabber's rope, freeing Pikachu. Agatha tells them to leave while they still can, but they stubbornly refuse. Jessie brings out Seviper while James brings out Cacnea to attack. Seviper uses Bite while Pikachu uses Quick Attack to dodge and grab onto Seviper's tail to throw it. Pikachu uses Thunderbolt to send Seviper flying back into the balloon. Cacnea uses Pin Missile while Golbat uses Supersonic to send it back at Team Rocket. Golbat uses Air Cutter while Pikachu uses Thunderbolt to send Team Rocket blasting off. Scott lets Ash know that they will be contacting him soon about the Battle Frontier and Agatha says she will support him all of the way.
Ash returns to his home in Pallet Town and is greeted by Delia, Misty, and Professor Oak. He's surprised to see Misty having an Azurill, and she explains that Tracey gave it to her as an Egg. Mimey also greets Ash and is holding Ash's lunch that he prepared. Ash hears a car horn and looks outside to see that Max and Professor Birch have come to visit him as well.