Cell of Empireo - A certain “0.5”

(manga adaptation of 2003 indie RPG title)
Haruki Atou is an investigator working for the Otowa Detective Agency. Atou is entrusted with taking care of his junior colleague, Shinano, who was found with amnesia. One day, Shinano suddenly disappears. The last place where his whereabouts were confirmed. It is near the facilities of the "Empyrean Heaven Institute," a religious organization that Atou was planning to investigate next. Atou is caught up in the horrifying reality of the Institute and the incident, but he soon realizes...

He wasn't involved by chance.

"Does thou enjoy the love of God?"