In a far distant future, humanity has embraced the Fractale system as the ultimate path towards utopia. Comprised of several trillion networked computers, Fractale was created in the 22nd century to promote a peaceful lifestyle for the entire world in exchange of a periodic recovery of personal data from individuals through terminals located within their bodies. Living in a rocky coast region, Clain is a young boy fascinated by old technology. After helping a girl named Phryne, she gives him a pendant before disappearing by the next morning. Accessing the data from the peculiar gift, Clain ends up summoning a girl-shaped avatar named Nessa. Together they start a journey as they discover the truth behind the Fractale system.