After a scientific experiment leads to the creation of a clone of Mewtwo, he sets out to destroy the world. Ash and his friends then decide to thwart Mewtwo's evil plans.

Yu-Gi-Oh! Zexal is a Japanese manga and anime series and the third main spin-off series of the Yu-Gi-Oh! franchise. The manga began serialization in Shueisha's V-Jump magazine from December 2010 and is licensed in North America by Viz Media. The anime series, produced by Nihon Ad Systems and Studio Gallop, aired on TV Tokyo between April 2011 and September 2012, following the previous anime series, Yu-Gi-Oh! 5D's, with an English-language version airing in North America between October 2011 and August 2013. A second series, Yu-Gi-Oh! Zexal II, began airing in Japan on October 7, 2012 and in North America from August 18, 2013. The series aired on The CW's Saturday morning cartoon block, Toonzai, and continues to air on its successor, Vortexx, later airing on Nicktoons from April 2013. It now airs every Sunday at 11:30,on Nicktoons.

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.

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!