X was a Pokémon Trainer child prodigy. But now he's depressed and hides in his room avoiding everyone--including his best friend Y. An attack on their hometown by Legendary Pokémon Xerneas and Yveltal, led by Team Flare, forces X outside... Now what?

Y and friends are attacked by Legendary Pokémon Yveltal while X and Blue are attacked by Legendary Pokémon Mewtwo! Why has Mewtwo come to Pokémon Village, a sanctuary for refugee Pokémon? And why is Mewtwo so angry? Then, the mysterious test subject trapped inside the Essentia Expansion Suit regains consciousness...