During the reunion with their old friend Misty, Ash and co. discover Hansen wants to rule the Togepi Kingdom and the Mirage Kingdom. Will they be able to stop him, and will Misty say good-bye to the Pokémon she cared for so long?

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?

Ash and co. reunite with their old friend Misty, who is happy to meet May and Max for the first time. Soon, they enter a kingdom dedicated to Togepi and soon meet Sara, princess of the Togepi Kingdom. Team Rocket also teams up with Colonel Hansen, who wants to rule the kingdom with an iron fist. What will happen to Togepi now, and has Max learned a way how to keep Brock from flirting with pretty girls?

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.

Ash challenges Flannery to a Gym match. Ash hopes to have an easy fight by using Corphish. Flannery, despite sometimes acting a bit nervous, manages to display some clever moves to thwart Ash's tactics and sends Torkoal, who switches offense and defense, pushing Ash to his limits.

On their way back to Mauville City, Ash and friends travel through the Valley of Steel, home of many different kinds of Steel Pokémon and a potential shortcut to Mauville City and then Petalburg City. On their way through, they come across a Torkoal being attacked by several Steel Pokémon. After using Pikachu to scare the Pokémon away, the Fire-type hears a noise, also scaring it off. Later, having reunited with Torkoal, Ash and friends become determined to help Torkoal defeat the Steelix that lords over the valley. Will they succeed in cutting through the valley unharmed or will the angry Steel-type block their way?

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.

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.

While doing her training with Beautifly, May's frisbee flies off. Torchic goes to retrieve the frisbee, but also finds a Skitty, who seems to be ill. May is amused by Skitty's cuteness and goes with her friends to a laboratory, where Skitty would recover through aromatherapy. Team Rocket plans on stealing the fragrances, but Meowth finds Skitty and falls in love with her. The heroes try to get the fragrances back, while Meowth starts wondering what he'll do with Skitty.

After Ash and Co. reach Lavaridge Town, they meet Flannery, the Gym Leader. Having just inherited the Gym from her grandfather and determined to prove her abilities, she is just as eager as Ash to battle, but the Gym's battlefield is full of holes and therefore cannot be used. Deciding to help, the gang are hard at work filling the holes. Meanwhile, Team Rocket are standing by ready to snatch one of Flannery's Pokémon, a Torkoal that they can give to their boss.

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 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.

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.

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.

After earning the Dynamo Badge from Wattson, Ash and co. continue their journey. May insists to go to Fallarbor Town while Ash suggests they go to Lavaridge Town. Max suggests they go to both and Brock decides the order. During the trip, they notice some watermelons float down by the river and have some lunch. Ash then comes up with an idea: Teach Treecko to use Bullet Seed like the Shiftry that attacked them a while back, and as practice, they try it by spitting watermelon seeds. Can Treecko learn to master this move, and who do the watermelons belong too?

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.

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.

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.

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?

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 come into the Banana Slakoth Garden, a famous tourist spot. However, they find it empty, save for a Snorlax, who is eating away the bananas. Marcel asks for their help and the heroes accept it. However, when they face Snorlax, it uses Yawn, putting everyone to sleep. To battle against such a foe, the heroes speak with Professor Oak, who shares some tips.

May reaches the second round of the Contest and defeats Jessica (who is Jessie, in disguise). Seeing Grace had managed to defeat her rival, Drew, May wonders if she could defeat Grace. During the battle, however, May displays new tricks she learned from Grace.