Set in a Japan 500 years after an endless war called Eternity was called to a conclusion by a miracle, people live in The Time after Eternity. A form of Christianity has spread and the Vatican now controls everyday life; people are divided into the "deeply devout" and the "not so devout". Miracle engineering powers the economy.

Ogito, though he is known for being godless, for some reason is taken in 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 priest—the head of his three person team—is killed, and Ogito is left only with the priest's weird apprentice Izumi: a man who gave up his life to God to let his heart reside in a puppet.

With endlessly creative art and world-building, this manga is a feast of the unusual and a flowering mystery quickly leaving your preconceptions behind.