After the events of Pokemon XY&Z, Serena decides to go to Kanto with Ash to compete in Pokemon contests. While they're in Pallet Town, however, they meet a 28-year-old trainer named Timothy who forms a rivalry with Ash and challenges him to compete in the Indigo League again. Thus, with Serena's permission, Ash joins Serena on her journey through the Kanto region. Along the way they come across Ash's former traveling companions as Serena competes in Pokemon contests and Ash rechallenged the gym where he didn't earn his badge properly.

But unknown to Ash and his friends, Timothy, his Raichu, Electchu, and his best friend, Coovers from the International Police, are on a mission to go through the Battle Frontier in order to find Brandon who may have found the Gieldanstone: a white jewel that makes Arceus itself obey the will of anyone who holds it. The two men and the Raichu are attempting to retrieve the Gieldanstone before Team Rocket gets it and uses it for their ultimate plan to finally control all Pokemon and rule the world.