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.