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?

With the help of another new ally, computer tech Cassius, our friends set off in search of Y's missing mother, Rhyhorn Racer Grace. En route, they are attacked by Y's former classmates from the Sky Trainer Training School! And then Y gets separated from the others...

Who is being mind-controlled by Team Flare this time...?!