From a birds-eye view, the setting of Delta Green might seem to have a problem in the sheer amount of conspiracies fighting or exploiting the Mythos. Those twelve guys in robes next to a freezer full of babies don't stand a chance, right? There's no way they can escape the notice of the FBI's Occult Crime Lab, the NSA's zombie-scanners, MJ-12's psychic monitoring systems...
This isn't actually what the books say, but plenty of people have gotten that impression both from people talking about DG as a setting, skimming the sourcebooks with all their 'Organization Resources' headers, and assumptions based on X-Files or other conspiracy-based RPG settings. And maybe actual campaigns, I don't know.
For myself, there's three lenses that I find the setting makes more sense, both in regard to a campaign's bureaucratic verisimilitude and a campaign's horror dramaturgy. And I use the word lens in both the 'rose-tinted' sense of giving everything an emotional hue, and the 'magnifying' sense of making clearer something hidden within.
The first lens is assuming that each agency has a very specific version of 'the supernatural' which is their lens for viewing strange things through. They don't perceive 'the mythos' as a cohesive set of things or an alternative cosmology (and Keepers shouldn't either, really), just a series of strange events. This human ignorance is partly the specifics of each groups' history, partly just human frailty, and partly the flying epistemological debris from the impact of any unknowable horrors.
• One of the parts of the setting that protagonizes Delta Green over the other groups is their—for lack of a better term—institutional paranoid schizophrenia. The history of types of contact with weird things they have had gives them a cult-centric focus, or one which tends to view the activities of supernatural beings as 'invasive' and 'infectious.' It's easier for them to identify patterns of bad weirdness: cults are isolated, travel in groups, hide their true non-homo-sapiens biology. The details of their practices and how they interrelate might be a mystery, but since the agents usually come from some sort of counterintelligence or criminal investigation background they can shift from crimes committed with a weapon to crimes committed with an alien servitor more easily.
• MJ-12 has an alternative mythos already, one which can deal with one half of the situation quite readily (anything that looks like an 'alien') but which might default to rationalization or total ignorance when confronted with a classical occult gloss to it (like trying to figure out a Resurrection spell).
• The Karotechia has the entirety of Aryo-Theosophy to frame their worldview, and lucky them, it's a lot of the same stuff which inspired/fed HPL et al in the first place. No wonder they make such good villains.
• PISCES, on the other hand, can be read as having a focus on identifying and exploiting or neutralizing human mutations, be they psychics or blessed of Shub-Niggurath.
• GRU-SV8's origin parallels Delta Green, and along with it can help them see the weird as an invasive or corrupting force, associated with cannibalism, the dead and the un-living, which leads to some version of classical criminal activity.
• M-EPIC is essentially a law enforcement version of the Residential Schools Act. (I'm Canadian so I might have more complex opinions about M-EPIC than the rest... also there's the [SPOILERS])
• One of the Directives From A-Cell, this one focusing on semi-aware mythos groups includes a cool idea for a French group whose 'exposure' consists of whatever they've stolen from MJ-12. This makes them second-hand dupes, and an illustration of how to draw in new groups without having to come up with a whole new overlay: they just steal someone else's.
A second lens through which to see Delta Green is that the history of these groups all stem from events that happen in the first half of the 20th century. (Glancy mentions this in the aforementioned Directive From A-Cell.) WWI birthed Delta Green and GRU SV-8, WWII fostered PISCES, the birth of the Cold War was the cradle of MJ-12—and I like to think that if any of those groups go down, there's not going to be anyone in the governmental sphere replacing them. They're becoming corrupted, breaking apart, or falling over each other.
In anticipation of the new DG RPG, I made a few alterations to the background for my last Delta Green game: replaced MJ-12 with a constellation of military contractors and biotech companies, which Kroft funnelled patents and materials into before being purged himself.
A third lens for our microscope of horrors—any of the above groups can be reinterpreted as an infection of a government by a cult. Most of them are already described as such. Others (i.e. Delta Green) can be turned into villains simply by taking their standard operating procedure to the ultimate extreme. Abducted by aliens? They shoot you. Found an artefact which has some weird snake glyphs? They smash it, your notes are stolen, and their friendlies in academia kibosh your future funding grants.
Without the proper magnification, the groups that make up the Delta Green milieu look fearsome and hardy, ready to take on all comers with ferocity. But when you get up close enough to peer into their cellular matter, you can see the weakness in their flesh.
While I'm here, I might as well plug The Unspeakable Oath to anyone who isn't already a buyer/subscriber. For $5 an issue you can get 60-odd pages of some of the finest horror roleplaying stuff being produced today.