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!

Fractale is based on and original TV anime series of the same title. On June 19, 2011, mangaka Mutsumi Akazaki stated in a blog post that she found working on the Fractale manga 'uninteresting' and added that she wanted to work on a manga that she enjoyed. The blog post was soon removed. As a result, the anime's director Yutaka Yamamoto requested the production committee to discontinue the manga series, though there was no indication that this was approved. Akazaki later apologised for the remark.