In the legendary past, before Poké Balls were made; 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 Cameron Palace in Kanto that would leave no survivors. He transferred this message to his master, the legendary hero Sir Aaron, while he was being attacked by a violent group of Houndoom. 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 Aura Sphere, he eliminated them. Though by the threat, the queen of Cameroon, Lady Rin was resolute to die with her civilians, and so Sir Aaron made a choice.

A comet bearing a deadly Pokemon creature crash-lands onto Earth, terrorising a nearby high-tech city, where Ash, Pikachu and friends are currently visiting...

Ash, Pikachu and his friends try and stop a pair of thieves hiding out in the canals and alleyways of Alto Mare, 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.

40 years ago, a Celebi was being attacked by a Pokemon Hunter. Luckily, a young boy named Sammy saved Celebi. Using its Time Traveling power, Celebi transported himself and Sammy 40 years into the future. There, Ash, Misty, and Brock assist Sammy to the healing lake in the forest so they can heal the wounded Celebi. Unfortunately an evil Team Rocket member, Viscious a.k.a. "The Iron Masked Marauder", tries to capture Celebi using his technology. As Ash and Co. try to get away from Viscious, they also run into Jessie, James, and Meowth, who also want to capture Celebi. Soon it becomes a race against time to get Celebi and Sammy back to the forest before Celebi is caught and is used to destroy the forest and themselves.

When Molly Hale's sadness of her father's disappearance get to her, 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 mom, Ash along with Misty & Brock invade the mansion looking for his mom and trying to stop the mysteries of Molly's Dream World and Entei!

The adventure explodes into action with the debut of Mewtwo, a bio-engineered Pokemon created from the DNA of Mew, the rarest of all Pokemon. Determined to prove its superiority, Mewtwo lures Ash, Pikachu and others into a Pokemon match like none before. Mewtwo vs. Mew. Super-clones vs. Pokemon. It's the ultimate showdown ... with the very future of the world at stake!