The Spanish Inquisition had nothing to do with the military, it was a court of law, or more appropriately a parallel judiciary power with a whole system of appeals, a supreme council, and very clearly determined duties: the Inquisition was responsible for judging the crimes of apostasy, heretic pravity, possession, ownership,distribution or production of forbidden books, etc. With time it got a few extra matters, like judging coin forgery, treason, and even piracy, which were crimes against the Crown.