Vatican City is a state held by the HolySee ,the ecclesiastical jurisdiction of the Catholic Church in Rome, the episcopal see of the Pope, and an independent sovereign entity. It oversees the Black Order and supports it in the Holy War against the Earl of Millennium through the facility of Central.
The Vatican is led by the Pope. He has command over the Catholic Church, and the Black Order.
The Cardinals are ecclesiastical leaders who are chosen by the Pope and are charged with assisting him. It seems like some cardinals are actively involved with the Central section and thus with the Black Order. They are considered the backbone of the Order 
Central is a facility located in the Vatican from which it oversees the Black Order. The Exact hierarchy of it is unknown but it seems to be composed with different divisions and some are similar to those of the Black Order.
- Zu Mei Chan (retired, deceased)
- Sahlins Epstain (deceased)
- Bridget Faye - Secretary (transfered to European Branch)
- Legory Peck - Scientist (transfered to European Branch)
- Mark Burroughs - Scientist (transfered to European Branch)
- Howard Link - Assistant (presumed dead)