The story takes place at the end of Kingdom Hearts 358/2 Days, Riku defeats Roxas to help his childhood friend Sora wake up from his slumber. With the help of Diz, an enigmatic man who knows too much about the heart, they tried to send Roxas into a Digital recreation of his town, changing his memories in the process, but the experiment goes wrong due to Roxas waking up earlier.

So to escape, our main protagonist summons a dark portal to get through, but part of the computer and the teleportation laser ends up overcharging Roxas portal sending him really far away from the universe, to a world where only ponies live. In this world, Roxas will learn the meaning of friendship and love by helping the mane 6 with her problems, but he is not alone, new foes will appear thanks to his keyblade so he will have to protect this new world with his life.