Backdrop: The city of "No. 6" is a tightly-regulated metropolis, whose citizens believe there is no better place to live in the world.
CH01: Shion is an elite HS student, and he's been singled out among all his peers to attend an elite program. One night, during a thunderstorm, a strange young man makes his appearance at Shion's house. The boy's name is "Rat" and his body carries a "violence chip" (VC). Shion should have contacted the authorities, but instead he attends to a bullet wound on Rat's shoulder. Shion is later contacted by the Public Security Bureau (Agent Yamase) because of his contact with Rat and because he failed to contact the authorities. For punishment, he and his mom are banished to "lost town", an outcast/slum suburb of the city. Shion ends up a common city park worker. He discovers a corpse in the park on day, and assumes the person (an old man) probably just died while out for a walk. However, the decay of the corpse is not natural. Also, there's a strange bee/wasp that flies out from within the body. A clue perhaps? Then another unnaturally decayed corpse is discovered. Then Rat reconnects with Shion and tells him to get out of the City. The "perfect city", Rat explains, is anything but that.
CH02: