In the not so distant future... Kisaragi Shirou, a man with a special power who lives in the slums. His power is only known to a limited group of people in the government. Topological Ghost (TG), the power to materialize digital objects into the real world. Shirou, his sister Aki and his brother Jin worked as test subjects in a TG research project funded by the government. But an accident during an experiment kills his sister and his brother disappears soon after. After leaving the research institute, Shirou begins to live a life of self-indulgence in the slums. Until one day, when he suddenly meets a girl who resembles his dead sister...