The clandestine agency (not bound to any one country) that protects the world (who, generally, is blissfully ignorant) from these threats is simply called the "Company".
The setting usually has players in the dangerous job of agents working for the company, or in the even more perilous profession of opposing the agency for whatever reason.
Individuals having undergone incredibly intense levels of training prior to their graduation, the black ops can be likened to the starring roles of classic action movies.
Beyond this basic expertise, however, each black op belongs to a department which encourages a specialized focus in a certain set of skills.
In contrast to their brutish exterior, however, most Combat Ops are as intelligent and refined as the rest of the academy's Graduates, and many are known to appreciate fine art and literature as much as they do their weapons.
The Security ops have the broadest training, allowing them to fairly judge the safety of any mission at any point in the operation.
The Technology ops are almost always called "techies" or "hackers", and have a reputation of being both geniuses and disaster-prone, due to their habit of tinkering with devices in the field, sometimes with mixed results.