On their way to Pacifidlog Town, the boat Ash and his friends are riding breaks down, forcing them to make a pit stop on Donto Island. It is currently the Donphan mating season, which they end up being separated from each other. May now has to make the ultimate decision: stay to find Max and miss the final contest before the Grand Festival, or leave alone for Pacifidlog Island trusting that Ash will find Max and come to the Contest for the next morning.

With the Hoenn League still underway, Ash and Tyson battle it out to decide which one of them will move on to the final four. Since Glalie and Sceptile are already knocked out of the competition, who will get the upper hand?

On his way home to Pallet Town after saying goodbye to his friends, Ash meets Scott, Leader of the Battle Frontier. After losing to Elite Four member Agatha, Scott tells Ash about the Battle Frontier. The latter agrees to take the challenge but first he must deal with Team Rocket and return to Pallet Town. After coming home, Ash meets up with his old traveling friend Misty.

Ash and May prepare for the challenge ahead of them in the Kanto region. May left two of her Pokémon with her parents at Petalburg City in Hoenn. However, before their new adventure, Team Rocket shows up to steal all of Ash's Pokémon and the group must fight to stop their dastardly plan. After stopping Team Rocket plans, May leaves one of her Pokémon with Professor Oak but a Squirtle chooses her as its Trainer and accepts it to her team. Ash also leaves two of his Pokémon he caught in Hoenn with Professor Oak as well but one of his from the lab decides to accompany him on his new journey.

Ash and his friends set out for Mt. Moon, home to the Cleffa family of Pokémon. However, the young Trainers are surprised when they spot a lone, distraught Cleffa.

Ash and friends save a morose Psyduck from a group of fighting-type Pokémon, Machoke, Machamp and Machop, that are pursuing it. Meanwhile, Team Rocket decides that the Psyduck would make a perfect gift for their boss.

The Battle Factory is Ash's next destination—if he can find it, that is. He and his friends have become lost, but they see snow and an Articuno flying overhead, followed by a plane in distress. The group winds up at a Pokémon Center, where Scott gives them a ride to the Battle Factory. There they meet Noland, who's not just the Factory Head but also a bit of a mechanical mastermind, and the pilot of the plane they saw last night. Ash can pick which of Noland's Pokémon he wants to battle. Noland has befriended an Articuno whom he helped once, and he takes Max and Pikachu up in his plane to fly with the Legendary Pokémon. Team Rocket wants Articuno for themselves, and they show up in their own plane to steal it. It's no match for Articuno, who quickly sends them on their way. Impressed, Ash decides he wants to battle Articuno. What's more, he wants to battle it with Charizard! It looks like this is shaping up to be quite a match...

After surprising everyone by choosing to face the Legendary Pokémon Articuno in his first Battle Frontier battle, Ash calls upon an old friend to battle it as he plans to use fire against ice. Will Ash be victorious in his first Battle Frontier battle.

The kids are heading to Maisie Island on a ferry when they spot a Spoink floating on a log. They quickly realize it's the same Spoink they helped before. When they save it and bring it aboard, it trips, dropping its pearl overboard. Ash's Pokémon go looking for the pearl with no luck. When they arrive on the island, they meet a scientist named Isaiah who is doing research on Clamperl and their pearls—which end up as Spoink pearls. The jewel of his collection is a rare blue pearl. Team Rocket sneaks in and tries to steal the blue pearl, only to be beaten out by Spoink stealing it first. Everyone goes looking for the little Psychic-type Pokémon. Meanwhile, the blue pearl accidentally gets switched with the pink pearl from a wild Clamperl. When this fact is discovered, everyone goes looking for the Clamperl and Team Rocket steals it away.

The heroes encounter a man named Adam who's searching for treasure. They decide to accompany him to find an old ship, which is told to have lots of treasure on it. Just as they take the submarine down, they also encounter Team Rocket, who is also determined to take the treasure, which is connected to the Relicanth Adam saw earlier.

The heroes come to the A-B-C Islands, where they meet up with Professor Birch. The Professor wants to study more about Clamperl's evolutions, Huntail and Gorebyss. They also accompany two children, who are angry at each other, for they want to evolve Clamperl that goes against their principles. Birch, however, finds something that can settle the trouble, and give Team Rocket a new opportunity at stealing Pokémon.

Since they have to wait for the boat to Mossdeep City, the heroes spend some time with other trainers, who want to get physically fit for the battles. While Brock, May, Max, even Team Rocket exercise, Ash has a Double Battle with the coach, Rocky, who shows how much his Pokémon can be in sync.

Due to a twist of fate, the heroes get captured by Team Magma and face their leader, Maxie. After Maxie explained his goals, Team Aqua's Shelly frees Kyogre and reports to her leader. In a moment of confusion, Pikachu takes the Blue Orb, which gets absorbed into him. Just as the heroes try to escape, Ash gets captured, while Team Aqua's leader starts controlling Kyogre. However, an unexpected help arrives, a man whom Ash and Brock have met before.

Team Aqua has gained control over Kyogre and prepares to unleash its powers over the world's water levels. A Blue Orb-possessed Pikachu releases Groudon from its entrapment and the two prepare to take on Kyogre in a battle to end all battles. Will Groudon and Kyogre destroy the world with their legendary battle or will Lance, Ash and his friends be able to stop the world's imminent destruction?

The heroes arrive in Mossdeep City, but learn the Gym Leader Ash wants to battle is at the Mossdeep Research Center. Once they arrive there, the heroes meet up with Tate and Liza, who just had a battle. Learning these two are duo of Gym Leaders, Ash is surprised he has to fight them in a Double Battle. While spending some more time at the space center, Max and Tate go to a space shuttle, only to encounter Team Rocket, who wants to steal the space shuttle.

Once again, the time has come. Ash will have a double battle against the terrific twins, Tate and Liza. As the battle begins, he sees they don't get along very well and the battle could be an easy win for him. That is, until Team Rocket interferes and snatches Lunatone and Solrock. After thwarting their latest plot, Rachel suggest that Ash and Liza and Tate continue their battle, even though the Gym is destroyed they could have it on the cliff. As the rematch begins, Liza and Tate are more in-sync than ever. Will Ash be able to beat them this time? The answer might shock you.

After battling a trainer, Ash, as well as his friends, meet Drake of the Elite Four. Drake is impressed by Ash's skills and invites the heroes to his boat, where Ash will have a battle with him. Just as everyone sees Drake doesn't do much, the latter makes his counterattack and shows Ash where he went wrong.

Arriving on an island, Max encounters a Cradily, an ancient Pokémon that is supposed to be extinct. His friends do not believe him, so Max goes to search for it and finds a building. Ash, May and Brock eventually find a woman and are surprised to see the Cradily Max spoke about. They go to the lab, where they also find an Anorith, which evolves into an Armaldo. Team Rocket barges in and after failing to catch Armaldo, who goes on a rampage.

As the heroes sail to May's next Contest, May finds a boy named Harley. She speaks to him a bit and meets his Cacturne and eats his cookies. Harley is annoyed at the girl, who becomes his rival that he wants to crush. During the Contest, Harley gives May some false advice, which May accepts, only to find out Harley tricked her. Just as she faces Harley, he uses another trick up his sleeve to deceive May even more, wanting her to be defeated.

Continuing their journey across Izabe Island, Ash and friends run into an old man who tells them the legend of the giant Claydol. When Team Rocket hears the legend, they unleash the Claydol that's going on a rampage.

While on their journey across Izabe Island, Ash and his friends meet a girl named Samantha, who performs her ribbon dance in various towns, and her Mawile, who develops a crush on Brock's Lombre. In the next town, Team Rocket takes Mawile, but ends up taking Lombre by mistake. Now Ash and his friends must save Lombre and Samantha's show.

While traveling on Izabe Island, Ash and his friends end up above a Trapinch Labyrinth. They meet up with two people named Elisa and Hal, two of the reserve rangers. After a Team Rocket encounter, they all end up inside of the labyrinth. Will they find a way to get out of this situation?

Still traveling towards Sootopolis City, Ash and friends arrive in a town where the people hate Absol. They blame Absol for all of the troubles that have in their small town. Ash and friends decide to help a kid named Nicky find his missing brother Gordon, who went to solve the mystery of the appearing Absol, as well as try to solve the mystery of the Pokémon themselves.

Still heading for Cerosi Town and the ferry to Sootopolis City, Ash and his friends stop at a Pokémon Center to stay warm as a blizzard approaches. At the Center, a wild Snorunt steals all 7 of Ash’s Badges. Will he be able to get them back or will he have to train all over again?

Continuing across Izabe Island, Max finds a sick Ralts. Brock is unable to fully cure it and they must bring it to the Pokémon Center. However, Team Rocket wants to capture the Ralts. Ash, May, and Brock battle Team Rocket while Max rushes to the Pokémon Center as quick as can. However, he must get there before it is too late, and has to deal with Team Rocket again and also Kirlia and Gardevoir.