Mikoto Misaka, one of the strongest Level 5 espers in Academy City, gave her DNA map to a certain doctor when she was young, believing that it may be used for greater good. Unfortunately for her, it ended up being used to create countless clones of herself; forming the Misaka network, in order to create the strongest esper by sacrificing these clones whom she considers as her own sisters.
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.
The year is Regild Century (R.C.) 1014. A millennium has past since the catastrophic end of the Universal Century era. Mankind has rebuilt itself and, through the lessons learned from the previous era, managed to sustain a long lasting peace. However conflict has once again arisen, resulting from disagreements regarding the world's only space orbital elevator, the Capital Tower, and its role as the sole means by which nations on Earth obtain energy. During a routine training session while ascending the Capital Tower, Capital Guard pilot cadet Bellri Zenam, tasked with protection of the Tower, fights off an attacking space pirate, Aida Rayhunton, and helps capture her mobile suit, the G-Self. Strangely, Bellri finds out that he is one of the only three individuals to be able to pilot this mysterious mobile suit. Seemingly chosen by the G-Self, Bellri is thus drawn into a brewing conflict that will have consequences for the entire world.