With the completion of the Fractale world administration system, humanity has, for the first time in history, attained a paradise where living is effortless.
Now, one thousand years after Fractale's activation, the system is still operational, but there is no one alive who understands it. The vast majority of people unquestioningly believe that its preservation is the sole condition to human happiness. On an island in the far corner of the continent Fractale begins to show signs of decay, though.
Clain is a boy who lives an aimless life. One day, he helps a girl, Phryne, who is being pursued by unknown assailants. However, she soon disappears again, only leaving a broach behind. The curious Clain successfully activates the antique data saved in the broach. And so, Nessa, a data avatar in form of a young girl, enters the boy's life.
Clain and Nessa leave on a journey in search for Phryne. In doing so, he will learn the truth behind Fractale.
