In the distant future, genetic engineering has been put to a much greater use in Konoha City's society. The LSOGA facility soon began its experiments on small animals like mice and rats, then they moved on to bigger animals like dogs and pigs, and then finally; human beings.

The result of the experiments created a new type of human; a Synthetic Humanoid Intended for Nocturnal Observation and Basic Infiltration, or "S.H.I.N.O.B.I" as they are called for short. These genetically modified humans are able to manipulate the energy around them and turn it into physical energy to heal or kill other human beings. However they also created another branch of S.H.I.N.O.B.I that known as S. (Synthetic Humanoid Mechs) which are people whose bodies are fused with parts from robots, turning them into unstoppable forces of strength, agility, and speed, and making them behave more like Machine-like than human.

Both of these man-made creations patrol the city, keeping order among the citizens.

But there is a much darker side to this project. Most of the S.H.I.N.O.B.I are young children, given to LSOGA by their parents or taken by force to live as mere experiments, never treated as actual human beings. This has caused much uproar in the city and sparked a resistance movement to free the children. Despite the rebellion being crushed by the Higher Ups, it is said that it still exists and lays hiding in wait to strike again. They may not know it, but the future of the city and the world is in the hands of 6 LSOGA subjects...