The story takes place on an island, where a "Fractale System" is beginning to collapse. One day, Clain finds an injured girl called Phryne under a cliff. She disappears leaving a pendant. Clain sets out for a journey with the girl-shaped avatar Nessa to look for Phryne and discovers the secret of the Fractale System.

In the future, the world is managed by a network called the Fractale System. A boy named Clain is living an aimless life with his parents, who are actually computer-generated "Doppels". One day, he runs into a pretty girl named Phryne, who is being pursued by someone. When he rescues her and helps to keep her hidden from her pursuers, he is pulled into her troubles as well. After meeting her, his life will never be the same! 

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