A year after the fall of Platinum Jail, the entire known world is destroyed by travelers from another world. The world of the dark, of the unseen entity in the shadows. For Japan and Midorijima Island, they are yokai, having migrated from their own dying world in giant floating ships. Six ships cover the region, one in particular being interested in Midorijima Island for one reason. The ship's lord was once wounded by a mortal man. That man created two children, twins, from the lord's genetics. And now he wants them back. Yet even in the strict harshness of yokai ethics and politics, one particular yokai finds his heart and body finally soothed for the first time in millennium.

As technology advances, the use of AllMates has dwindled amongst the government and higher echelon. Jobs formerly done by lower-class humans have been replaced with androids. Government couriers and bodyguards, even police AllMates, have been replaced with something on the more disturbing side. Genetically altered humans, known as Anima. Though expensive, their worth outlives that of former workers and AllMates. Instead of spending a week in the shop, Anima heal one another in mere hours. Anima don't need to be paid, and hold undying loyalty for those they serve. Most of all, Anima cannot survive without a Limiter, a human who serves as their leash, much like a master to an android. Anima cannot turn on a Limiter. Thus, Anima cannot turn on humanity.

Two years after the breakdown of Oval Tower and Platinum Jail, the island is bought out by another power-hungry man. Only this time, he controls by fear. The Tech Squad, consisting five powerful androids, constantly patrol the island. The citizens hide simply when seeing one of these figures, and new rules are put in place. The homeless are killed without question, so Clear has begun living with Aoba out of fear. But while on the way to go hangout at their usual spot, Aoba, Clear, Koujaku, and Noiz run across one of the androids, known to the public as.... Green Heart.