The war on terror exploded, literally, the day Sarajevo was destroyed by a homemade nuclear device. The leading democracies transformed into total surveillance states, and the developing world has drowned under a wave of genocides. The mysterious American John Paul seems to be behind the collapse of the world system, and it's up to intelligence agent Clavis Shepherd to track John Paul across the wreckage of civilizations and to find the true heart of darkness—a genocidal organ.

Gyakusatsu Kikan was originally in production by studio Manglobe and was intended to be released on November 13, 2015. However the studio filed for bankruptcy on September 29, 2015 and production was handed over to Geno Studio. The film was reported to have been 60% complete by Manglobe before their production ended, however producer Kouji Yamamoto stated it had really been 20% complete.