When Lawrence III's scheme to capture the Legendary Pokémon Lugia upsets the balance of nature, it is up to Ash Ketchum and his friends to save the world.

When the sadness of her father's disappearance gets to Molly Hale, she unknowingly uses the Unown to create her own dream world along with Entei, who she believes to be her father. When Entei kidnaps Ash's mother, Ash — alongside Misty and Brock — invade the mansion looking for his mom and trying to stop the mysteries of Molly's Dream World and Entei!

In order to escape a greedy Pokémon hunter, Celebi must use the last of its energy to travel through time to the present day. Celebi brings along Sammy, a boy who had been trying to protect it. Along with Ash, Pikachu, and the rest of the gang, Sammy and Celebi must encounter an enemy far more advanced than the hunter, with the fate of the forest hanging in the balance.

Ash and friends (this time accompanied by newcomer Dawn) arrive at an idyllic village on their way to their next Pokemon contest, where chaos will soon erupt with the prophecy of two Pokemon Gods (Dialga and Palkia) and the arrival of a mysterious, seemingly deadly Pokemon named Darkrai, which has the power to distort space and time.

Ash, May, Brock, and Max come upon the festival of the Wishing Star of Seven Nights. During their enjoyment, the legendary Pokemon--Jirachi, descends from the heavens and befriends Max. Jirachi, with the power to grant any wish, is sought after by many people wanting to claim its power. One man seeks to use its legendary power to revive an ancient Pokemon known as Groudon, unaware of the dangers hidden within Jirachi's powers

In the legendary past, before Poké Balls were invented, an aura-guiding hero Pokémon named Lucario sensed two groups of armies about to clash, and a threat of a massive war in front of Oldoran Castle in Kanto that would leave no survivors. He transferred this message to his master, the legendary hero Arlon, while he was being attacked by a violent group of Hellgar. During the battle, his sense of sight was lost and he was rendered unable to see. He used the detection of his Aura, and so with the offensive Wave Bomb, he eliminated them. Though by the threat, the queen of Rota, Lady Rin was resolute to die with her civilians, and so Arlon made a choice.

On their way through the Battle Frontier, Ash and friends meet up with a Pokémon Ranger who's mission is to deliever the egg of Manaphy to a temple on the ocean's floor. However, a greedy pirate wants the power of Manaphy to himself.

After accepting an invitation from a mysterious trainer, Ash, Misty and Brock meet Mewtwo, an artificially created Pokémon who wants to do battle.

Ash, Pikachu and the gang try and stop a pair of thieves hiding out in the canals and alleyways of Altomare, the age-old water capital. Joining the adventure are two new legendary Pokémon, a pair of siblings named Latias and Latios, who serve as peacekeepers and protectors of the Soul Dew — a priceless treasure with a mysterious power.

Ash, Pikachu, and their friends come to a desert city by the sea. Here they meet the Mythical Pokémon Hoopa, which has the ability to summon things—including people and Pokémon—through its magic rings. After a scary incident, they learn of a story about a brave hero who stopped the rampage of a terrifying Pokémon long ago. Now, the threat that has been bottled up for years is in danger of breaking loose again.