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.
Lupin begins his heist by stealing a newly-discovered Japanese cultural treasure being transported to Germany. During his attempt to steal the treasure, however, he witnesses the always-ambitious Zenigata's supposed "death," a plan hatched by a ninja clan who are also after the treasure. Can Lupin and his friends prevent the ninja clan from obtaining what they seek?