The story is set in the early 21st century with the population decimated by bio terror. Two kinds of humans now exist. One is the Nokusu who were infected with a virus but survived and consequently they carry an antibody. Most are young, healthy and have high intelligence, but they have a high sensitivity to ultraviolet rays and are active mostly during the night. The other group are the Kyurio. They survived by never having the virus. The Nokusu discriminates against the Kyurio. Tetsuhiko Okudera is a Kyurio. He was born in a poor village. He isn't happy with being a Kyurio and wishes he could be a Nokusu. Yui Ikuta is Tetsuhiko’s childhood friend. She tries to revive the poor village.

In the dawn of the Meiji period, the Gokumonjou, an inescapable prison, has been established in the middle of an enormous lake to counter the soaring crime rates the new era has brought. Serving as the ferrymen are the famous Kumou brothers: the eccentric family head, Tenka; the reckless but noble second son, Soramaru; and the guileless youngest, Chuutarou. In spite of their grim work, the three lead relatively peaceful lives in the ever-cloudy town of Oumi, together with their housekeeper, Shirasu Kinjou. But buried in the long history of Oumi is the legend of the terrifying "Orochi," a serpentine beast that awakens every three hundred years in a human vessel. Unbeknownst to Soramaru and Chuutarou, the actual job of the Kumou family is to seal the Orochi away before it fully revives—or the world will be plunged into destruction. Amid the monster's next resurrection, the Kumou family must find the resolve to keep laughing under the clouds.

The year is 2XXX and Keiko Town is an over-industrialized stretch of blackened factories pumping out thick layers of smoke that cast it in a perpetual state of semi-darkness. The citizens of Keiko Town fare no better and walk around their dilapidated town in a stupor of hopeless despair. In an abandoned factory in an obscure corner of town lies the secret base of Hikari Club. The teenage boys of Hikari Club despise the adults of their community and have taken it upon themselves to eradicate what they perceive to be the evil and filth of the grown-up world. To accomplish this, they build a machine with artificial intelligence and dub it “Litchi”. However, with the boys on the cusp of puberty and turning into adults themselves, their own world has begun to collapse around them.