After a practice battle between Ash's Chimchar and Dawn's Piplup, Chimchar begins to cry because Ash was nice to it even though it lost, and Paul wasn't. Things get worse when a trio of Zangoose attack and Chimchar has to face its fear and eventually defeats them and overcomes its fear of Zangoose. Chimchar also receives some unexpected advice from Meowth about the future.

Gardenia reappears in a town, organizing a special exhibition battle for the town's children. She teams herself with James of Team Rocket in a match against Ash and Dawn. She proposes that James should leave his Cacnea with her to train when he is unable to use it to its full potential. He eventually decides to accept the offer.

Buizel is more interested in Ash's gym training, and Aipom is more interested in Dawn's contest training. Thus, Zoey suggests that Ash and Dawn do a trade.

After Ash's Buizel destroys the Hallowed Tower, a Spiritomb is unleashed and attacks Ash, Dawn, Brock and a nearby village. Then Jessie tells it that Ash is a descendant of the Aura Guardian that coincidentally has a Pikachu, that sealed it away. So Ash sets out to stop the Spiritomb and with Pikachu's help, they seal it away in the Hallowed Tower.

Ash's group encounters a Pokémon Breeder working on the construction of a stone bridge. The woman is arguing with the bridge's designer because of their Pokémon assistant Bibarel's refusal to work. After the stone cutter returns, Bibarel begins to construct the bridge, with help from the gang.

Ash battles Alan, a trainer that wants his Nosepass to evolve into a Probopass, but it can only evolve if it levels up in Mt. Coronet. When it does, Team Rocket brainwashes it and now Ash & Co. have to get it back.

Ash encounter a young Officer Jenny named Marble and her Luxray. Luxray is unable to use its electric moves, so Ash & Co. set out to help it.

In Solaceon Town, Ash's group meets up with Dawn's old friend and rival Kenny and his new Pokémon, Breloom. Kenny tells them he is going to the Solaceon Ruins, a place of worship for the legendary Dialga and Palkia, so they tag along, only to get more than they bargained for when the Unown that live in the ruins become furious along with the appearance of the sinister Team Galactic. Among the chaos, Aipom evolves into Ambipom

Dawn competes against Kenny in the Solaceon Town Contest, looking for redemption after her crushing loss in Hearthome City. Jessie of course enters. Dawn loses once again and Kenny and Jessie face-off in the finals. Jessie defeats Kenny and wins her first ribbon. Zoey tells Dawn that the overuse of Swift caused Ambipom to be no longer seen and the point of an Appeal is to show off the Pokémon.

On their way to Veilstone City, Ash and his friends stop off at the Mountain Hut Maid Café for a nice drink of Miltank's Milk. However, when they arrive, they learn of the troubles the Café is having, being under-staffed. Ash and his friends offer their services and soon become Maids in the Café. Brock helps Autumn, the youngest of three sisters bond with her Miltank, Ilta. All the while Dawn is trying deal with her feelings of losing a contest for a second time.

Ash and his friends stop at a Hot Spring managed by Dawn's childhood friend, Leona. Both girls are happy to meet again, but when Dawn and her friends want to go to the hot springs, they find out that there isn't any water. Because no water is coming from the spring, the group want to investigate, along with Leona and her Swinub.

Ash and company visit a town where it is plagued with a group of Gligar led by a Gliscor. Ash and friends help Officer Jenny try to remove the flying Pokémon, while Ash's rival Paul sets his eyes on capturing Gliscor. In the end, Paul captures the Gliscor on his team, and Ash captures one of the Gligar that keeps showing up.

When our heroes' Pokémon are having a fun time in a sandpit, a Hippowdon appears from within. However, the over-curious Pachirisu can't help peeping into the Hippowdon's mouth and accidentally falls into it. The situation gets worse when Hippowdon becomes the target of the Team Rocket duo Butch and Cassidy.

In the forest just outside Veilstone City, the group witness a young female martial-artist and a Lucario in a fierce battle. The girl is revealed to be Maylene, the city's Gym Leader, at which point Ash immediately asks for a Gym Battle. However, she recently lost to Ash's rival Paul, and is depressed over her defeat. Further insight into the matter is revealed by Reggie, Paul's older brother. Reggie also helps Ash's Staravia learn Brave Bird.

Dawn challenges the gym leader of Veilstone City, Maylene, in hopes of helping Maylene get over her defeat. Maylene defeats Dawn and she and her Lucario regain their confidence.

Maylene finally accepts Ash's challenge. Ash uses Staravia, Chimchar, and Buizel against Machoke, Meditite, and Lucario. The battle between Buizel and Lucario ends up in a tie but Maylene still gives Ash the Cobble Badge.

With Ash acquiring the Cobble Badge, our heroes decide to spend the night in Veilstone City before heading out. Reggie takes the group to a park with several meteoric stones lie. However, Team Galactic appears and try to steal them for their world domination plans.

While training Gligar, Ash hears singing. When they look to see who is singing, they meet a magician named Francesca and her three Chingling. Francesca is trying to get her spoiled Chingling to have a better attitude.

On their travels, Ash and his friends meet up with another Pokémon Ranger—Kellyn—and a Riolu. It turns out that Hunter J is after Riolu, due to its ability to use Aura Sphere before evolving. Ash and Riolu start to bond with their shared Aura, but J is insistent on getting it. This episode relates to the secret mission in Pokémon Ranger: Shadows of Almia, from which the player can transfer a Riolu that knows Aura Sphere to their copy of Diamond, Pearl, or Platinum.

Hunter J has managed to kidnap Riolu. But despite that, Riolu, reveals his whereabouts to Ash, using its Aura. With Rangers Kellyn and Solana joining them, Ash and his friends go to hunt down Hunter J and get Riolu back. However, J is far more formidable than anyone could have anticipated. Will Ash and friends be able to return Riolu back to its kingdom?

Ash and Co. arrive at a lakeside Pokémon Center. Jessie's Dustox sees a shiny Dustox, and follows it to the lake. Jessie releases her Dustox, allowing it to mate. This is related to the Season 1 episode 21, "Bye Bye Butterfree" where Ash releases his Butterfree so it can mate with a pink Butterfree.

Ash and his friends meet Sho, a boy who has a Pichu and a Raichu. He mistakes Ash's Pikachu for a wild Pokémon. Just like at the Vermillion City Gym, Ash and Pikachu have the option again to evolve Pikachu to Raichu, after a loss to a stronger opponent. Paul witnesses this defeat and scolds Ash for losing to such an opponent, but manages to redeem himself of that defeat in a rematch.

Ash, Brock and Dawn meet the Champion of the Hoenn Region, Wallace. He says he will be holding a Pokémon Contest and the winner receives a ribbon that can be used anywhere. The group spends the day with him, resulting in advice from Wallace for Dawn to play with her Pokémon more and for Ash to enter Buizel in the contest. At the end of the episode, Ash receives a phone call from his friend, May.

Ash and Brock's old friend May, still training to become a Top Coordinator, visits Sinnoh for the Wallace Cup. Upon arrival at the Seven Stars Restaurant, they find out that only those who win a tag-battle against the restaurant's owners can eat there. Ash partners with Brock and win the double combat with a single move. Before Dawn and May's combat, Team Rockets steals all food from the restaurant. May and Dawn partner up and defeat both the Team Rocket and the restaurant's owners, the later by using Blaziken and Piplup together to create a fantastic fire/water combination. There is a cameo from Drew, Harley, and Max.

Ash and his friends have arrived at the Lake Resort where the Wallace Cup will take place. Zoey also arrives, and competes, too. Right when the contest began, Dawn becomes nervous and has trouble keeping her composure. Meanwhile, May decides to enter with Wartortle, and Ash enters with Buizel. There are cameos of Drew, Harley, Max, Norman, Caroline, and Solidad.

At night, Ash takes a walk near the Lake Valor with Pikachu when suddenly, something in the center of the lake begins to glow, and it turns out that Azelf appears. When Ash tries to approach it, the shadow disappears again. The next day, the second round of the Wallace Cup begins. May's Venusaur is then revealed, and there is a cameo appearance of May's Skitty battling in the second round. Dawn, May and Zoey make it to the semi finals but Ash loses to a tough coordinator called Kyle. After it is Dawn's turn to battle Kyle in the semi-final, she uses Piplup against his Crawdaunt. There are cameos of Norman, Caroline, Max, Kenny and Paul.

Dawn beats Kyle and May beats Zoey in the semi finals and both have to battle in the finals. In the finals, Dawn faces-off against May in the Wallace Cup. Dawn uses Piplup and May uses her Glaceon. Dawn manages to narrowly defeat May's Glaceon by a fraction. After the contest ends, Dawn earns her second Ribbon! Now that the contest is over, May departs from Ash, Dawn, and Brock once again and goes back to Johto.

When on their way to Pastoria City, Ash and friends meet a trainer named Tyler that wants to catch a Yanma. But Team Rocket ends up catching it after he weakened it. After Jessie captures the Yanma and sends it to Giovanni, who rejects it, she decides to train it herself and it quickly evolves into Yanmega.

Ash and co. are running after Gligar who has been blown away by a gust, and promptly run into Paul. After a huge argument about their different ways of treating Pokémon, Ash challenges Paul to a battle. But when Chimchar is battling Paul's Ursaring, it activates an overpowering blaze. Chimchar also gets confused and starts randomly attacking anyone in its path.

After Ash & Co. arrive in Pastoria City, Crasher Wake refuses Ash's request for a battle because he has to take care of something. They tag along and find out there is a Croagunk Festival in the Pastoria Great Marsh.

At the Pastoria Gym Ash challenges Crasher Wake to a 3-on-3 Gym Battle using Pikachu, Turtwig and Buizel, while Wake uses Gyarados, Quagsire, and Floatzel. However, Pikachu accidentally shocks Buizel and this causes them to argue which makes a difficulty in helping Ash defeat Wake. Suddenly, thanks to that Buizel had rescued Pikachu from the attack; their argument concludes. Ash manages to defeat Wake and he earns the Fen Badge.

A Swinub shows up at Mr. Backlot's mansion and starts to eat all the Poffins. Dawn tries to stop it by making her own Poffins for Swinub. Dawn ends up capturing Swinub at the end of the episode.

Ash continues his training with Gligar, but finds out it has become fearful of battles since the battle against Paul's Gliscor. The group meets Gary again, and Ash asks Gary to help him solve the problem with Gligar, and Gary gives Ash a Razor Fang, which makes Gligar evolve into Gliscor.

Ash and friends return to Hearthome City to challenge the Gym Leader who was gone during their last visit. However, they hear that the Gym Leader is still gone, making Ash unable to have his fifth Gym Battle. The group meets Paris, a Pokémon Stylist, and her Lopunny. She suggests that Dawn should enter the Hearthome Collection, a famous fashion show.

While traveling through a deep valley, Ash and friends encounter a swarm of Psyduck in the middle of a road. Upon trying to pass them, the Psyduck suddenly start attacking them, and to make things worse, when ash and team try to battle them there are too many to battle so ash sneaks behind them with the help of gliscor only to know that psyduck is trying to protect their families who are waiting to hatch their eggs and doesn't want people to interrupt. when team rocket tries to steal the pokemon with the help of psyduck they manage to blow them away and saves the day. Ash and team goes to check psyduck's home lake they find mug has taken the lake, ash and team fights the group of mug and takes back the lake for psyduck

When Ash & Co. are invited to attend a Pokémon Academy, they decide to enter it. For their first task, they choose a PokéBall that contains a Pokémon inside. The trainer then has to train the Pokémon and be able to use it in battle. The gang then meets Angie, and meets Conway again.

While at a Pokémon Academy, Ash, Dawn, Brock, Angie, and Conway find that their Pokémon are becoming hypnotized when they go near a lake. So they decide to go and investigate what's going on.

While Ash and friends are training at the Summer Academy, they are taught how to deal with Ghost-Type Pokémon, should they ever run into them. They are then paired up to find a hidden treasure. While searching, Conway has a run-in with a Dusknoir.

After the Trainers are finished with the training, they must use a Pokémon to bring them across a rigorous track to the finish line. Finally after a tough competition Ash and Pikachu came first, and Angie and Shinx came second which led to the victory of the red team. Everyone is given a certificate. They said good bye, and the team continued their journey.

On their way to Celestic Town, Ash and his friends have to take Piplup to the Pokémon Center after it collapsed from over-excessive training. Meanwhile, Team Rocket, who were following the group on a slope, decide to have lunch in a luxury restaurant. But then Jessie notices that Meowth's golden charm is buried under rolls of flab. The trio now realizes that, due to them having led a rich and luxurious life ever since they had earned the money at the summer school, they have become lazy and grown a lot in flesh. Wanting to return to their former "sharp and cool" shapes, they start a harsh training session.

Zoey is facing a critical situation against a very tough coordinator. With her Glameow confused, the battle ends quickly. Ash and co. cheer for Zoey who was defeated by the mysterious trainer. This mysterious trainer is none other than Fantina, who like Hoenn's Juan is a coordinator and the Hearthome Gym Leader. Ash requests that he battle her and she accepts. How will this battle turn out? And can it prepare Ash for his actual Gym Battle?

Brock is away on an errand. When they can't handle it, they send Gliscor to bring Brock back. Brock finds he can't carry Gliscor back, as it can't glide in the wind going the opposite direction, and leaves it, promising to return for it. At the end of the episode, the gang comically realizes that they left Gliscor behind, and scene shows a frustrated Gliscor with a long way to go.

Dawn has entered the latest contest held in Celestic Town. Dawn meets her mother's old rival Yuri, that wants to win this contest. When she and her mom's rival "Lila" (Yuri in Japanese version) come face to face in the Finals of the contest Dawn has to give it all she has to win. Dawn wins the Celestic Town ribbon and her third contest ribbon.

Commander Mars and Cyrus (not known yet by Ash and co. that he is a part of Team Galactic) debuted in the anime along with Commander Saturn and the other Galactic grunts . In this episode, they steal the Lustrous Orb and the Adamant Orb from the Celestic Town museum for the power to awake Dialga and Palkia in their future plans.

In this episode Commander Jupiter is introduced. Ash and the gang are helped by Cynthia to stop Team Galactic from stealing the Lustrous Orb and the Adamant Orb, but they fail because they had no idea how large Team Galactic was.

Arriving back in Solaceon Town, the gang meet up with Angie at her Parent's Daycare. She tells them her parents are gone for a while, so she leaves the daycare to her for a while. Ash and the gang tell her about the strange monster terrorizing Solaceon Town. She later reveals that the monster is a Lickilicky that she evolved from a Lickitung which she taught it Rollout. So the gang goes out and helps her find the Lickilicky and bring it back. At the end of the episode, it is revealed the Angie may have a crush on Ash.

As Ash and the gang are heading back to Hearthome City, they encounter Aaron, a member of the Elite Four. They see that he's training his bug Pokémon, but also himself. He explains to the gang that he's trying to look for a Wurmple he released as a child as he felt it could become stronger on its own, but he wants him back. The gang offers to help Aaron look for his released Wurmple. They find Aaron's Wurmple, but since then it has evolved into Beautifly. The two become a team again. In the end, Aaron happily says thank you and a farewell, and Ash and his friends head on to Hearthome City.

Ash has a battle with Paul. Choosing a one-on-one battle, Paul chooses Honchkrow, and Ash chooses Turtwig. Honchkrow manages to drive Turtwig into a corner, but at the last moment, Turtwig evolves into Grotle. However, Grotle loses all its agility and loses to Honchkrow anyway. Paul then reveals to Ash that he has already obtained the Hearthome City gym badge. Afterwards, Brock confronts Paul that he met his older brother Reggie over a missing Frontier Brain symbol, which in turn, partially reveals Paul's captious nature of becoming strong. Grotle gets up late that night and unsuccessfully tries to regain its agility. Paul's Torterra shows up and comforts Grotle by showing it that speed isn't everything about battles. Torterra tells Grotle that it can also rely on defense. Torterra shows an example with Ash's Gliscor using a Steel Wing straight to the head. Torterra emerges unscathed, and Grotle resumes to its normal behavior.

Upon arriving at the Hearthome Gym, Ash and his friends run into Barry, a trainer from Twinleaf Town. Barry turns out to be an admirer of Paul, whom he saw when watching the Double Battle Tournament. Ash challenges Barry to a Pokémon battle. Ash chooses Chimchar, Gliscor, and Pikachu, against Barry's Staraptor, Roserade, and Empoleon. Ash manages to narrowly defeat Barry, finishing off Empoleon with Pikachu's Volt Tackle.

The Gym battle between Ash and the Hearthome Gym Leader Fantina has begun. Ash chooses Buizel to battle Gengar, Chimchar to battle Mismagius, and Pikachu to battle Driftblim. Using his new counter-shield strategy Buizel defeats Gengar, Chimchar defeats Mismagius but Pikachu gets defeated by Driftblim when Fantina uses her own strategy against him, Buizel also gets defeated by Driftblim, but Chimchar finally defeats Driftblim, and Ash wins the Relic Badge. Barry, having seen Ash defeat a Gym Leader he lost to, declares that Ash is a rival if Ash can beat the leader of the Canalave Gym. Meanwhile, Jessie, as her alter ego, Jessilina, wins her second ribbon using her Yanmega in the Majolica Town Contest!

Ash and company, along with Barry, take a ride in a blimp to Canalave City. When they arrive, Team Rocket, disguised as photographers, trick them into taking a picture of all of their Pokémon, which actually turns out to be a net to kidnap them. The Pokémon fight back to attempt to escape, and everyone's Pokémon (including Team Rocket's) gets blown away into the sky in the process and they all get separated. A chase ensues when Team Rocket declares that whomever should find the Pokémon first, gets to keep them all. When Meowth is grouped with Pikachu, Pachirisu, and Mime Jr. after the explosion, he considers leaving Team Rocket for good. Can all of the Pokémon find their trainers?

The group heads to the Canalave Gym, but they are told that the Gym Leader isn't there right now. At a police station, the group is told by Officer Jenny that all the people in the town are having nightmares, and that the cause of the nightmares seems to be the Pokémon Darkrai. Also, Dawn's Swinub evolves into Piloswine in order to stop Team Rocket from stealing Cresselia.

Learning that the Unova League will be held at Vertress City, Ash and his friends prepare for the tournament, but not before making a detour towards Iris' hometown, the Village of Dragons. But along the way, Iris drags the boys and their Pokémon into competing against a group of women who believe that their Pokémon are not only powerful but more beautiful than anyone else's.

On the way to the Unova League, Ash and Cilan get challenged to a Tag Battle against the brothers Soren and Rocko who have trained their Braviary (Soldier of the skies) and Drilbur (Warrior of the land) to perform amazing combination attacks.

On the way to Vertress City, Ash, Cilan, and Iris find their way to Iris's hometown: the Village of Dragons. While there, Iris shows Axew to her elder and helps her childhood friend Shannon when one of her Zweilous suddenly evolves into Hydreigon and goes out of control.

The gang arrives in Opelucid City for Iris' scheduled rematch against the Dragon Master and Gym Leader Drayden, who handed her and Excadrill their first-ever defeat years ago. Upon arrival, Iris remembers her difficult time in going to school there and trying to adjust to urban life. She and the others then travel to the Opelucid Gym for her rematch with Drayden, where she puts her Excadrill and Dragonite to the test, respectively, against Drayden's Haxorus and Druddigon in order for him to evaluate her training and skills.

Near Vertress City, the gang meets the Pokémon Rescue Squad's Virgil - trainer of Team Eevee - and his brother Davey, whom they decide to assist in helping a group of troubled Cryoganal.

The Unova League begins, and as the preliminary round matches get underway, Ash finds himself up against Trip.

Ash's battle against Trip continues, with Pikachu facing Serperior. As the preliminaries end and the first round begins, Bianca pits her Escavalier and Emboar against Cameron's Samurott and Riolu.

During a break in the competition, Iris's Axew follows a balloon and gets lost in Vertress City. Pikachu manages to track him down, but they are cornered by a group of Trubbish and their Garbodor leader.

The third round of battles at the Unova League begins and Ash finds himself up against Stephan, putting Krookodile, Palpitoad, and Leavanny up against Stephan's Liepard, Zebstrika, and Sawk.

In the fourth round of matches, Ash battles against Cameron - who begins the match by revealing his secret weapon, Hydreigon.

Ash's Snivy and Pikachu must face off against Cameron and his newly evolved Lucario.

With the Unova League tournament over, Ash and company return to Nuvema Town to meet up with Professor Juniper and to tell Professor Oak about his results. Along the way, they meet Nanette who is going to see Juniper for her first Pokémon, and eventually chooses Tepig and asks to have her first battle with Ash. However, during the battle, a robot appears and it is piloted by a very familiar trio. Later, Professor Juniper gets a call from her father, who invites Ash and friends to visit him at the White Ruins, located north of Icirrus City.

On a boat heading to see ruins dedicated to Reshiram, Ash, Iris, and Cilan meet the mysterious boy calling himself N, who quickly befriends their Pokémon. However, when Team Rocket attacks the group once more and James's Amoonguss paralyzes Pikachu with Stun Spore, N's timely intervention helps turn the tide of the fight.

The group's boat arrives in Aspertia City, and they arrange to meet Cheren, Professor Juniper's acquaintance and the city's new Gym Leader. A teacher at the local Pokémon School, Cheren is lacking in confidence regarding his worth for the title, something Cilan - as a former Gym Leader himself - connects with him over. After misadventures in the Pokémon House on the school grounds - including a series of mishaps between Cilan, Pansage, and a flock of Ducklett - Ash has an unofficial Gym match against Cheren, Oshawott facing off against Herdier.

When Team Plasma scientist Colress uses his machine to draw out Pokémon strength, the controlled wild Pokémon attack the residents of nearby Floccesy Town. Ash, Iris, and Cilan get caught in the middle of the mayhem when Pikachu and Axew also fall under his control, but when they are saved by Looker, they agree to aid him in his investigation of Team Plasma and Colress's scheme.

While stopped at Floccesy Ranch, Iris's Dragonite helps rancher Elly's Ampharos get into the fighting spirit.

Ash and friends once again run into N, who has freed a Braviary held captive by Team Plasma. They help him bring it to a Pokémon Center, but when Braviary is tracked by a pair of Team Plasma Grunts - Nero and Bianco, who respectively use a Seviper and Zangoose in battle - N puts his life on the line. Successfully freeing Braviary, N joins the group on their journey to the White Ruins.

Upon returning to Virbank City, Ash and friends meet Halsey who runs a rescue team consisting of his two Frillish, his Dewott, and his Watchog. Making his personal feelings on the idea of Pokémon putting themselves at risk for the sake of humans known, N's belief that Watchog (who seems ill-suited for the Team's risky endeavours) is being used as a tool causes an ideological clash between Halsey and N, but the two young men must put their enmities aside when a fire breaks out in Virbank City's Industrial Complex.

Ash and his friends come across the Kanto Fair, and seeing a Charmander perform on stage reminds him of his old friend Charizard. He tells Iris, Cilan and N about his and Charizard's history, with Misty and Brock making cameos during the tale. Professor Oak sends Charizard over, and after he meets Iris' Dragonite, the two trainers agree to have a friendly match. Ash's offer to let Charizard rejoin his team is met with approval from all parties involved.

Colress appears and tests his newly-advanced machine on Dragon-type Pokémon - first taking over a young trainer's Haxorus, and later Iris's Dragonite. As Ash and Charizard try to stop them, N puts himself in the crossfire, knowing the Pokémon should be friends and not fight.

After N is hurt by Colress's machine, two young women, Anthea and Concordia, come to save him. It is from these two girls that Ash and the others learn the truth about N's life, including his link to the evil Ghetsis.

Team Plasma's Colress convinces Team Rocket's Jessie and James to use his technology on Meowth to make him stronger, but it is all part of Colress's plans to test his Pokémon controlling device.

At the ruins dedicated to the Pokémon Reshiram, N steals the Light Stone from Cedric Juniper, and Ash's attempt to stop him ends with them separated from the others. Team Plasma move to attack the White Ruins while Team Rocket watch on in anticipation, and Iris, Cilan and Looker attempt to fight off the enemy forces.

Ash and N prepare to save Iris, Cilan, and Professor Juniper's father from the clutches of Team Plasma before Ghetsis can revive Reshiram, but their attempts to fight back are hampered by Colress's Pokémon controlling machine, forcing them all to call back their Pokémon. Pikachu gets hit by the machine's beam, which sways N into surrendering the Light Stone in exchange for its freedom just as Ghetsis arrives, ready to begin the ritual.

As the revived Reshiram quickly falls under Ghetsis' control, Ash and friends try to develop a strategy to stop Team Plasma. Looker convinces Team Rocket to help in the fight against the villains, while Ash and Pikachu aim to destroy the controlling machine, and N hopes to pacify the enraged Reshiram before it destroys the world in a righteous fury - akin to when it burned down Team Plasma's castle in the past.

With Team Plasma defeated once and for all, Ash decides it is time to go back to Kanto. Iris and Cilan decide to go with him to further their skills, and Professor Juniper charters all of them a cruise through the Decolore Islands on a boat with a mysterious crew. Once settled in their cabins, however, Ash finds that they are locked in and their Pokémon are not with them.

The cruise makes a stop on Honey Island, known for its colonies of the Honeycomb Pokémon Combee, Pupa Pokémon Kakuna, Stinger Pokémon Beedrill, and its honey-flavored cuisine.

As Ash and his friends prepare for the upcoming Marine Cup Tournament on board their new cruise ship, the group learns that Mrs. Ripple, a jewel collector, will display her collection after the tournament, but upon the tournament's conclusion she discovers that her rare Eye of Liepard has been stolen. She suspects Mr. Shaw - a businessman and jewel collector who has been asking to buy the Eye of Liepard from her - even though it was watched over by her Watchog all night. Cilan takes on his detective role once more to discover the thief of the Eye of Liepard.

On Scalchop Island, Ash's Oshawott goes up against the Dewott named Caesar to see who will win the battle at the Scalchop King Competition.

On the way to Mahora Island, the gang's boat passes through fog and they believe they see a familiar shape in it. After avoiding a giant Heatmor when Pikachu's attacks do not work against it, Axew gets poisoned by a Foongus's Mushroom Spore attack, forcing the gang to take him to an old Pokémon Center which they soon discover is operating illegally.

Ash, Iris, and Cilan catch up with Professor Oak who has come to one of the Decolore Islands to investigate the Plasma Pokémon Rotom and its Forme Change capabilities. However, the Rotom native to the island are more interested in Pikachu, Emolga, and Stunfisk.

When Team Rocket tries to ransack the group's cruise ship's food store, they are thwarted by a group of self-styled pirate Pokémon group made up of a Croconaw, an Octillery, an Azumarill, and a Ducklett, leaving Ash to try to get the food back.

On Wayfarer Island, Ash and his friends see the native Metapod and Butterfree, and when they find a Caterpie who has not yet evolved, Ash takes it upon himself to help the very lazy Pokémon join the rest of its friends, remembering the times he had raising his own Butterfree years ago.

On Capacia Island, after a Dunsparce Ash fails to capture and hurts Axew, Iris gets so mad at him that she says she will no longer be Ash's friend and leaves.

Ash, Iris, and Cilan take a break on Capacia Island only to discover they have arrived on the one week once every 1000 years when Jirachi awakens and grants a wish. Gemma, a young girl who lives on the island, wants to ask Jirachi to bring prosperity back to the island, but Team Rocket has other plans.

Ash must find a way to stop Beheeyem from taking over a town on Capacia Island after the townspeople, Iris, Cilan, and even Pikachu are placed under the strange Pokémons' control.

While on Harvest Island, Ash and his friends meet the Pokémon Reporter Alexa, who has come all the way from the Kalos Region with her Gogoat and Helioptile. She has come to investigate Harvest Island's fruit harvest festival, which the others realize has a Pokémon Sumo tournament. Ash, Iris, and Cilan enter Pignite, Pansage, and Dragonite in the tournament to win the grand prize Focus Band.

Alexa tells Ash, Iris, and Cilan about Yashi Island, a desert island where a pirate ship crashed years ago, and the ship's treasure has never been found. The group decides to investigate, and Team Rocket follows to get the treasure for themselves.

On Cave Island, Ash and his friends meet up with Clair, Gym Leader of Johto's Blackthorn City, who has come to the island to capture a different-colored Druddigon, but her Dragonite left without her. When they find her Dragonite, Iris's Dragonite takes an instant dislike to it and the two fight, hampering Clair's plans to find the different-colored Druddigon on the other side of the island from the port.

The appearance of Woodate Comet approaches, so Ash, Iris, Cilan, and Alexa go stake out the ruins where the legendary hero it is named after first spotted it. However, they must deal with several Ghost Pokémon and Team Rocket who are once again trying to capture Pikachu.

On another island, Ash, Iris, Cilan, and Alexa meet a boy named Tony who touches Alexa's Gogoat's horns, causing it to temporarily bond with him. They all help Tony meet his father on the other side of the island.

After being scolded by Iris, an ambush by Team Rocket starts to make Emolga wish she did not have to be with such strict trainers and fights on Team Rocket's side.

Chili and Cress meet up with Cilan on Paladin Island as they have both been beaten by a challenger at the Striaton Gym named Morana who exclusively uses Ice-type Pokémon such as Mamoswine and Glalie. It is up to Cilan and Pansage to face off against Morana and her Abomasnow for the honor of the Striaton City Gym.

The group finally reaches the waters off of Kanto, just as Team Rocket once again tries to do their best to take Ash's Pikachu.

With Iris and Cilan heading off on their own adventures in Johto, Ash is restless and still wishes to become a Pokémon Master. To that end, Alexa suggests that he travel with her back to her home in the Kalos region just as Team Rocket hatches another plan to steal Pikachu.