With the completion of the Fractale System, for the first time in history mankind no longer has to work in order to survive and they stepped into such an incredible paradise.

1,000 years have passed.

The system remains operational, but no one is able to comprehend it anymore. Most people have no doubt that only preserving the system can guarantee mankinds security. The story begins when Fractale starts to break down, at a small island in the corner of a certain continent. One day the boy Clain, who usually idles away his days, rescues a girl, Phyryne, that fell off a cliff after begin chased by someone. Clains heart skips a beat when he meets the girl. But then, Phryne disappears in front of Clain leaving only her broach behind. The girl-shaped avatar Nessa is locked up in the data left inside the broach and together with Clain they go on a journey to search for Phryne. That is when he begins to learn the secrets of the System.