X was a Pokemon 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 Pokemon Xerneas and Yveltal, led by Team Flare, forces X outside... Now what?

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