X, hiding from media attention after winning the Pokm̌on Battle Junior Tournament, is compelled to come out when a pair of legendary Pokm̌on and a shady organization attack his hometown of Vaniville.

"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 of Vaniville Town by Legendary Pokemon Xerneas and Yveltal, led by Team Flare, forces X outside... Now what? X, Y and company meet Trevor's online friend Professor Sycamore...but X is suspicious of him. Trevor sets out to get his Holo Caster repaired by Lysandre...who turns out to be another...

X is depressed and staying in his room, seeing no one. Then there is an attack on the hometown of X and Y and they must spring into action.

After Korrina's Key Stone is stolen, X retreats from the world again and holes up in a tree, but when Team Flare's secret headquarters is discovered, he reenters the fight.

Y and friends are attacked by Yveltal and X and Blue and attacked by Mewtwo. Nobody is sure why Mewtwo came to Pokemon Village or why Mewtwo is so angry. Meanwhile, the test subject in the Essentia Expansion Suit regains conciousness.