500 years after the conclusion of an endless war known as "Eternity," Japan has entered a new era. In this time after eternity, the Vatican has gained control over daily life as Christianity spreads throughout the land. Society has become divided between the deeply faithful and the less devout.
Despite being labeled as "godless," Ogito is chosen to intern in the "miracle inspections" department of the "department of saints." His vast knowledge of forbidden literature lands him on a team led by a priest, tasked with inspecting miracles. Things take a turn for the worse when the head priest is killed during an inspection, leaving Ogito alone with the enigmatic and strange Izumi. Izumi is reputed to have given up his own life to God, with his heart now residing within a puppet.