När Ashs Treecko och Corpish möter Grovyle och Slugma i en dubbel-strid, ser Treecko till att få övertaget genom att lära sig använda Bullet Seed.

En Tränare lär sig att Pokémon-strid kräver mer än bara taktik och teknik. Under tiden drömmer en Bagon om den omöjliga drömmen om att kunna flyga.

En inbjudan till Togepi-festivalen gör att Misty kommer till Hoenn-regionen, och då får hon veta att i ett kungadöme som ligger där, regerar de sitt land genom att följa infall från Togepi som passerar förbi.

Våra hjältar möter en ond regent, som vill använda Mistys Togepi för att stjäla tronen från den rättmätiga arvtagaren!

Ash, Brock, May och Max måste alla arbeta tillsammans, när de möter fyra medlemmar ur en familj som består av skickliga Pokémon-Tränare och deras kraftfulla Pokémon.

Våra hjältar uppdagar en kärlekshistoria mellan två Tränare som uppträder med sina Pokémon i en lokal dans-festival.

Efter att hon hittat en utmattad Skitty, överlämnar May den till ett lokalt aromaterapi-lab, där den återhämtar sig helt och hållet.

En gammal bekant vinner självförtroende och stärker banden till sin Zangoose, när han tvingas möta Seviper i en strid som är allt annat än rättvis.

Max träffar på en annan liten pojke som heter likadant som han, men som är väldigt olik honom till sättet. När den här nya, unga och oerfarna bekantskapen ger sig iväg på egen hand, måste Ash och hans vänner spåra upp honom.

Medan May förbereder sig inför sin andra tävling, möter Ash hennes rival Drew i en träningsmatch före tävlingen.

May ställer upp i sin andra tävling, där hon möter en mystisk medtävlare som är misstänkt lik en viss medlem i Team Rocket…

Ash och hans vänner träffar på en gammal kompis, som sedan de senast sågs har gått med i en Pokémon-hejaklack. När de bevisar att hans hejaklack inte är hederlig, blir Tränaren inspirerad att fortsätta sin resa istället.

När Team Rocket hotar en gård med Numel, jagar Ash och hans vänner iväg dem genom att Mays Skitty använder Assist för första gången.

När Team Aqua och Team Magma strider om kontrollen över en meteorit som finns uppe på ett berg, måste Ash och hans vänner sätta stopp för deras lömska planer.

Ash har knappt hunnit börja sin strid mot den nykläckta Gym-ledaren Flannery förrän Team Rocket avbryter, och striden blir uppskjuten med en hel dag.

Ash strider för sin fjärde Gym-badge i Hoenn-regionen! Kommer hans Corpish att kunna besegra Flannerys team, som helt består av Eld-typer?

När rykten uppstår som säger att en viss Spinda gör så att den som är Tränare åt den blir lycklig, kläcker Team Rocket genast en plan över hur de ska kunna stjäla denna lyckobringande Pokémon!

Ash och hans vänner kämpar sig fram genom en dal, som vaktas av lokala Stål-typ Pokémon.

Medan Ash använder sin nya Torkoal i en vänskapsmatch mot Gym-ledaren Wattson, möter May hans assistent med sin Skitty.

När Mays Skitty blir skadad och de är långt ifrån Pokémon-center, kommer en mästare i konsten Pokémon-massage till undsättning!

När Ash och hans vänner får veta att en maskerad medtävlare försöker tävla i hemlighet, hjälper de den blyga killen att dölja sin identitet.

I Pokémon-tävlingen i Vendanturf Town, möter May och hennes Skitty den maskerade medtävlaren som bjuder på en tuff uppvisning tillsammans med sin Dusclops!

The heroes, who are thirsty, wander the land. Brock shows them a spring, but it ran out of water. They go to the village, but find it deserted. Just as Lotad falls in a well and gets risen up, it evolves into a Lombre. Much to the heroes' surprise, the villagers start coming out of their houses and pray to Lombre and start cursing a Solrock, believing it is the reason for the local drought. In order to prove them wrong, the heroes decide to investigate.

The heroes, who got lost in a forest, encounter a Swablu, who has its wing injured. Along with the help of a local ranger, Morita, May spends time with Swablu, who recovers and heals its wing. However, due to its trauma, Swablu cannot fly, so the heroes try certain ways to teach Swablu how to fly once more.

During a break, the heroes get their lunch eaten by a Gulpin. They soon find out a group of Gulpin is eating away the food supplies in the city. They contact Nurse Joy and Officer Jenny, who receive help from Professor Jacuzzi, who decides to stop the Gulpin. After driving off the Gulpin, the professor uses a machine to launch Gulpin away. However, the machine malfunctions and oversizes Gulpin and Ash's Treecko, who battled the former.

Ash and friends are eating lunch in the woods when they notice that Treecko has wandered off. After failing to convince the Grass-type to come down from a tree, lunch is disrupted by a rampaging Loudred. Its Trainer, Guy finally catches up with his Pokémon and makes it stop.

Ash and Guy decide that both troublesome Pokémon need exercise, so they battle. While battling, both Pokémon evolve at the same time, into Exploud and Grovyle. The battle continues, but Exploud won't listen to Guy. It hits Grovyle hard and runs off.

Grovyle catches up with Exploud at a waterfall, and the two begin to battle again. Exploud still won't listen to Guy. Team Rocket interrupts, trying to capture Exploud, but Guy protects his Pokémon. Pikachu and Exploud send Team Rocket blasting off.

Guy and Exploud reconcile, and Ash and Guy decide to finish the battle.

While having sandwiches for lunch, the heroes are visited by a man named Poncho and his Ludicolo. They challenge Ash to a battle, who bets his sandwiches with Poncho, who is to buy cheeseburgers if Poncho loses. Corphish volunteers for the battle, but it seems distracted and eventually loses. This infuriates Corphish even more, who runs off while the heroes try to find out why Corphish is angry.

As the heroes arrive to Petalburg City, May and Max are visited by the crowd, who like Norman, Caroline and their children. While Max and May are dealing with the crowd and Ash battles a lot of trainers to prove he is worthy to challenge Norman, Team Rocket decides to disguise themselves to take profit from the situation.

Just as the heroes return to Petalburg City, Ash goes to the Pokémon Center to get ready for his Gym match, where he encounters Norman talking with Nurse Joy. Back home, May and Max, along with Brock, meet up with Kenny, who reports trouble. Caroline, Norman's wife, greets them as well, but something troubles her as well. Deciding enough is enough, Caroline goes with her children, as well as Kenny and Brock, to face Norman, who is hiding something. Ash, however, is at the greenhouse with Norman's Pokémon and faces Team Rocket, who want to steal them.

Ash faces Norman in a Gym battle. Norman switches offense and defense to baffle Ash, who tries to overcome this trial, having his Pokémon use abilities in the battle. After the battle, however, Max becomes upset over something.

The heroes decide to stop at Professor Birch's lab. Hearing Professor Oak will come to the lab as well, Ash and Brock decide to accompany Birch to escort Oak to the lab. However, Professor Oak arrives by a cart and greets May and Max, the latter being a big fan of his. Once Team Rocket steals Birch and Oak's Pokémon, May, Max and Professor Oak decide to go after them and rescue the Pokémon on their own.

Due to May being late, Ash is outraged, since he wants to go to Fortree City as quickly as possible. May becomes angry as well and soon, Ash and May are challenged by a couple named Oscar and Andi. Even during the battle, Ash and May bicker at each other, causing them to lose. Team Rocket gets challenged as well, causing Jessie and James to annoy each other. Just as they meet up with the twerps, James sides with Ash and Jessie with May to have another Tag Battle, which displeases Brock, Max, Pikachu and Meowth who just want the feud to end.

The heroes get lost in a forest. Just then, May gets taken away by a Skarmory. As Ash, Brock and Max try to get May out of the forbidden area, May befriends a Bulbasaur, but the other Grass-type Pokémon start attacking her.

With Bulbasaur being in May's team, Ash decides to call his own Bulbasaur to meet up. However, Team Rocket has modified the transporting machine, causing them to obtain the Poké Balls that are being transported. While Team Rocket blasts off during the battle, they manage to steal the Poké Balls. Fortunately, Ash's Bulbasaur returns and teams up with May's Bulbasaur to find Team Rocket.

While resting by a lake with his friends, Ash polishes his Badge Case and remembers all the Gym Battles he's won so far. Suddenly, a wild Whiscash jumps out and eats the case. Ash dives in to go after it to get his badges back, but nearly drowns. He is saved by a Fishing Master named Sullivan who has spent years trying to catch the giant Whiscash. Determined to retrieve the badges, Ash and the others start fishing. Meanwhile, Team Rocket are also trying to get a hold of the same Whiscash.

While separated from his friends, Ash encounters a girl and her Baltoy. He learns they were called to meet someone at a set of ruins, and her Baltoy is a key.

Arriving in Rubello Town, May finds Drew, who is going to participate in the Contest. She also meets Savannah, a wife, who is going to participate in the Contest. However, Savannah becomes nervous and asks for help from May, who has decided to use Bulbasaur, even if she didn't train it much. Since she can't compete without a ribbon, Jessie plans on stealing some.

May, confident in her Pokémon, enters the Rubello Contest with Drew and Savannah. While all three manage to pass the first round, May's Bulbasaur becomes nervous, which shakes May's victory. May tries to get Bulbasaur to battle, but this does not impress the judges or her friends when she takes her wins for granted instead of showing concern for her Pokémon's health.

Continuing their journey to Fortree City, Ash and friends come across a Spoink, who is upset after losing the Pearl it keeps on the top of its head. After Spoink tries to put on a couple of round Pokémon on its head, the Pearl is found. However, during a Team Rocket encounter, they steal the Pearl. After coming across a fair, James is approached by the same Magikarp Salesman who has made his life miserable in the past and offers to trade a Feebas for the Pearl. After discovering Feebas evolves into Milotic, Team Rocket agrees. However, when they let their new Feebas out to have a swim in a nearby river, they discover the Feebas is just a Magikarp painted with a Feebas' colors, meaning they have been swindled yet again. After Ash and the others find out what happened, they have to get Spoink's Pearl back by finding the Magikarp Salesman before Team Rocket do.

As they arrive to Crossgate Town, the heroes learn there is a tournament involving Flying-type Pokémon. May, Ash and, surprisingly, James, enter the competition. Just as James and Ash advance to next rounds, Jessie and Meowth decide to make another attempt at stealing Pokémon.

The heroes and Team Rocket, after another clash, have gone to the mansion. There, May argues with Max, who runs off and meets a Shuppet. Due to his fight with his sister, Max decides to play a prank on her, Ash and Brock with Shuppet. However, Team Rocket arrives and stirs trouble.

As the heroes have a meal, Torchic and Corphish start fighting. As Ash and May try to calm them down, Team Rocket arrives, and so do some Breloom, from whom they stole some apples from. The Breloom attack and blast everyone away, causing everyone to get separated. Max, Meowth, Torchic and Corphish try to find others and come to dead end, where they face the Breloom once more. Corphish decides to protect Torchic, who gathers all of its bravery to attack.

The heroes spend a day at the Weather Research Institute. Just then, Team Aqua, with Shelly as the commander, arrive to gather information about Legendary Pokémon. The heroes make a plan to protect the data, but an unexpected betrayal is among the scientists.

After the events that transpired at the Weather Institute, Ash and co. finally arrive at Fortree City. Ash couldn't wait to challenge the Gym Leader, sadly the Gym Leader is helping with the Feather Carnival. Later they meet the Gym Leader, Winona, who scheduled in Ash's request for a Gym Battle, but in the meantime they should have some fun. Meanwhile, Team Rocket has plans of their own. What sinister plot are they up to this time, and why does the carnival bring back such bad memories for James?

The time has come once more. Ash is ready to have his Gym Battle with Winona. Before the battle starts she evokes a prayer to all Flying Pokémon to give her strength. And now the battle begins. Will Ash fly high in the sky or will he crash and burn?

As the heroes continue onwards, they encounter a man pushing his Camerupt. After helping the man, the heroes are told the man, named Elijah, goes around villages and shows movies. The heroes decide to accompany them, while Team Rocket plans on stealing his equipment.

The heroes arrive in a deserted town and get rejected by Nurse Joy to stay in her Pokémon Center. They soon find out the PMC, Ken and Mary, whom Ash and Brock encountered in Johto, are here after a mysterious Pokémon. Arriving in the Pokémon Center, the heroes encounter Team Rocket, as well as the mysterious Pokémon, Lunatone. They soon find out Lunatone is weak and can be restored if it sees moonlight beams. While the heroes go to the place to heal Lunatone, they encounter the PMC guys again

After another encounter with Team Rocket, Ash loses Pikachu. Pikachu, however, has hit his head and suffers from amnesia and is found by Meowth. Meowth takes the opportunity and states Pikachu was one of Team Rocket members. Pikachu starts believing and once Ash comes to him, Pikachu turns his back on him. Ash, however, does not give up on Pikachu and tries to find a way to bring his memories back.

As they arrive in Lilycove City, the heroes meet Kelly, a fellow Coordinator, who knows how to make good Pokéblocks. As Max stays with Ash, who wants to teach Swellow Aerial Ace, Brock goes with May, who wants to learn more about Pokéblocks from Kelly.

May's Combusken manages to control the Fire Spin attack it launched. Through luck, May enters the next round with Kelly and fights Josaphine. In the final round, Kelly battles May, who has a tactic to overcome Grumpig's psychic powers. Just as Grumpig and Combusken are to fall down, May makes an honorable gesture. Meanwhile, Ash misses the contest to help his Swellow learn Aerial Ace.

Due to a mistake, the heroes sail away to an island, with their actual destination being Mossdeep City. On the island, they find Jimmy, who trains to become a judge. With teacher Serena's help, Jimmy tries to be the referee of a Double Battle of Ash vs. Brock. After the battle, Jimmy recalls his past before he has to rescue his Pokémon, who were stolen by Team Rocket.