The Vatican is an independent city-state theocracy in europe. While much is known about its public-facing facilities and functions, not much gets out about its primary functions that operate within the catacombs beneath.
The Vatican's private functions are twofold; recover and hoard saint corpses, which do decompose but never rot away past mummification, and to purify anomalies that the pope himself considers a threat to the continued semi-existence of the Godhead. Opertaives are often picked from death row inmates from neighbouring countries and given a baptism that prevents them from defying the church using water with an anomaly that makes it painful for them to act against the church.
The Vatican also has a massive stockpile of advanced weaponry, ranging from a flamethrower that runs on the spirits of believers being converted into holy fire, to fully sapient Jesus-like automatons that house the bodies of saints and beat sinners to death with wooden crosses once released into an area.