Professor Sycamore investigates the origins of the XYZ legend with Alexa about the story of a man named Jan and his love interest named Aira. A prophecy made long ago predicted that Yveltal would appear and drain all life from Kalos. Upon the arrival of Yveltal, Aira becomes fossilized as a statue while defending Jan. Afterwards, Yveltal enters into its long term sleep. Jan searches out Xerneas to restore life to Kalos. Years later, Xerneas reappears and does so. However, Aira is left as a statue. Many years later, Jan can be seen as an old and blind man. Jan discusses how he sleeps in the same spot every night. Jan talks to the Aira statue about how Xerneas and Zygarde made the forest so beautiful. Jan cuts an image of the "Z" symbol for Zygarde with a Zygarde Cell on it. Jan falls asleep for the last time. Jan says, "I want to be with her. I will sleep a little".
A young boy named Ash Ketchum embarks on a journey to become a "Pokemon Master" with his first Pokemon, Pikachu. Joining him on his travels are Brock, a girl-obsessed Rock Pokemon Trainer, and Misty, a tomboyish Water Pokemon Trainer who may have a crush on him. Ash and Co. end up traveling through various regions, including Kanto, the Orange Islands, and Johto, and then enter the Pokemon League competitions there.
Along the way, they run into many confrontations with Jessie, James, and Meowth, a trio of Pokemon thieves who are apart of an evil organization called "Team Rocket". But every time Team Rocket try to do their evil deeds, they fail thanks to Ash and his Pokemon.