US Government Department of Eschatology

While the general population of the world remains blissfully unaware of the existence of the supernatural, one cannot expect the governments to remain blind and deaf to that. Certain countries developed governmental branches manned entirely by the Initiates, acting as stereotypical Men in Black. They tend to focus on counter-acting major supernatural incursions, going after hostile cults and containment of various terrible artefacts. With a track record that can be described as 'varied'.
By nature, such organizations have a rather complicated relationship with their general government. When your president, ministers and 99% of the officials cannot perceive your existence, it makes working together awkward at best. As a result, most of such national organizations operate mostly on their own, though with certain procedures in place that allows them to temporarily gain the help of other governmental organizations.
As one can expect, there are cases of such paranormal governmental groups de facto controlling their governments. There are also cases of them falling into Power-worship, making them de facto cults. This state typically lasts until self-destructive behaviour natural to most cults dismantles their power base, they are overthrown by still loyal agents, taken down by other Initiates, or summon something that they can't control. And promptly stop being a problem.
The United States Government Department of Eschatology is an example of such an organization. It's known for both its ruthless efficiency and long-term suspicions of being a particularly successful archon cult, dedicated to preserving the world (or, to be exact, the United States population and its government) until the world ends in the way that its patron desire.

Structure

Department of Eschatology serves as a joint command centre for many subsidiary organizations dealing with the paranormal within the territory of the United States of America. Or on foreign ground, for as long as it threatens the interests and/or survival of the United States. It is composed of the Secretary of Eschatology, the Council of Twenty and regular staff, divided between several sub-departments.
Members of the Council of Twenty and the Secretary of Eschatology are mysterious. Their names remain hidden from the world at large, instead of using their titles during meetings with outsiders and lower-ranked members of the Department. No one is fully sure how they are elected (if they are elected at all). Some speculate them to be survivors from the last Thaumaturgic War, some claim them to be immortal masters of magic even beyond the level of magisters, and some suggest that they might not be humans at all. At least one theory suggests that the only mystery are their identities, as they are regularly replaced, with the masquerade created to maintain the air of secrecy.
Its subdepartments vary from human resources through artefact containment to dealing with Initiates committing crimes against mundanes while taking advantage of the Censor's Veil.
DoE possesses its own intelligence organization - the Supernatural Investigations Office, tasked with investigating domestic supernatural threats. This primarily includes cults and more organized predations of the supernatural threats (such as larger and more established groups of ghouls).
It also has possesses its own armed forces. Those, naturally, aren't counted under the US Army due to the US Army command being incapable of perceiving their existence due to the mechanisms of the Censor's Veil. These groups include the Non-Standard Assault Recon units (best described as Delta Force, but with way more stressful work environment and some magical support) and the 13th Infantry Division for large-scale operations against supernatural incursions and perimeter containment.

Majestic-12

There is a long-term conspiracy theory claiming that Majestic-12 (a 'mundane' conspiracy theory referring to an unknown government organization responsible for dealing with the Roswell Incident) is an actually existing, highly secretive body within the Department of Eschatology. However, what exactly is it and what it is capable of remains unknown. Whether it actually exists remains unknown.

Public Agenda

Official goal of the Department of Eschatology is the continuous existence of the United States, its population, way of life and the government despite the supernatural threats. This is a goal that it manages to a satisfying degree, given the fact that the country still exists, although it's far from being stable. The continuous warfare between the DoE, and the numerous cults and supernatural entities are at the very best an extremely costly stalemate.
Many speculate that this is at least partially amenable to the long-term goals of the Council of Twenty and the Secretary of Eschatology (or, perhaps, of the Majestic-12) himself, suggesting them to be cultists of archons working to maintain the existence of Mankind until an unspecified 'True End' comes. Various versions of these conspiracy theories exist, some claiming the end-goals of the Council being benevolent, while some are... quite the opposite.

History

The US Department of Eschatology was created in 1947, following the events of the Second World War. This is suspected by some of the more exotic scholars to be connected to the events of the concurrent Thaumaturgic War, which is however pure speculation on their part. It was less 'created' and more 'reformed', with several pre-existing organizations dealing with supernatural matters and connected to the US Government merging into one group.
Oddly enough many documents, photographs and artefacts appear to be suggesting that DoE existed ever since the inception of the United States as a country. This discrepancy is typically left unanswered, with Council of Twenty being particularly interested in erasing all evidence pointing towards it.