Set in a future Japan, 500 years after an endless war called "Eternity" was called to a conclusion by a miracle, people live in "the time after eternity". Christianity has spread and the Vatican now control everyday life; people are divided into the "deeply devout" and the "not so devout".
Ogito is known for being "godless" and is taken as an intern in the "department of saints" in the "miracle inspections" section, partly due to his reading many forbidden books. He is immediately taken off on an inspection where a preist - the head of his three person team - is killed, and Ogito is left only with the wierd Izumi - a man who gave up his life to God to let his heart reside in a puppet.