How to keep secret societies with super technology from taking over the world?

Question

There are a lot of fictional settings that have some sort of elite peacekeeping organization that is tasked with keeping people safe or keeping things "normal" and are frequently depicted as being above ordinary law in some way. The SCP Foundation or Men In Black are perhaps the two most extensive examples, but there are others such as the Marvel Universe's SHIELD, the Spectres in Mass Effect, Inquisitors in Warhammer 40k. Most of the time these organizations are presented as "the good guys", or at least the side that has audience sympathy, due to being the protagonists. This ignores the fact historical cases of organizations with the ability to use "whatever means necessary" in the name of the greater good with little to no accountability usually rapidly become corrupt and self-serving (SIDE in Argentina is the first example that comes to mind for me, but there are a lot of others throughout history).

This potential for abuse of power in elite organizations that see themselves as above the law is magnified when you give these organizations have principal dominion over anomalous technology or other supernatural or alien MacGuffins. As an example, consider the SCP Foundation. Even discounting everything the SCP Foundation ostensibly has to do "for the greater good" (e.g., Procedure 110-Montauk), the SCP Foundation is characterized by horrific abuses of power. They regularly prop up totalitarian dictatorships, interfere in presidential elections, assassinate high-profile individuals, participate in human trafficking, and use political prisoners, refugees (including children), and (formerly) African slaves as disposable test subjects. The SCP Foundation has committed genocide and xenocide against innocents to levels that would make the Imperium of Man proud. The leading council are incredibly corrupt, often abusing MacGuffin technology for their own benefit or having people killed and/or tortured to keep their power secure. This isn't even counting genuine accidents where they mistakenly torture and kill innocent people and are never held accountable for it. They have an ethics committee, but despite their fearsome reputation the SCP ethics committee is regularly unable to curb genuine abuses of power. However, the status of the ethics committee just highlights one thing: the only real check on the SCP Foundation is the SCP Foundation.

Most notably, governments and other nation-states have no control over the actions of these groups. The SCP Foundation answers to no government body or intergovernmental organization, and in fact regularly manipulates governments and large corporations to keep themselves in power. The SCP Foundation claim to exist to protect "normalcy", but this ignores the fact that they define what "normalcy" is. They suppress societal and technological developments as they see fit, and have even been mentioned to be suppressing human technological development to keep them controllable, preventing a societal or technological shift that could threaten their power. The only real check on their power are the other anomalous secret organizations in their setting, but that only highlights how the setting is a playground for the secret societies where ordinary people (or really, governmental bodies representing the people) have no real power to change things.

This isn't unique to the SCP Foundation, the SCP Foundation just explores the consequences of this in more detail than most works. The MIB are a less extreme, but not much better example. In the movies and spin-off television show the MIB manipulate human society as they see fit to uphold their mostly self-appointed mission of keeping alien life hidden on Earth. Human society is mostly unable to make their own choices because the MIB can edit memories as needed to manipulate societal evolution. For example at the end of the television spin-off the existence of aliens is revealed to the world, humanity seems to be accepting of it, but the MIB still neuralize the population to return things to the status quo. They're even worse in the comics, manipulating humanity explicitly for their own selfish benefit rather than the greater good. Similarly, SHIELD isn't much better (see: the entirety of Captain America: The Winter Soldier, Marvel Comic's Civil War, or Project Cadmus, SHIELD's DC equivalent).

What the point of all these examples are is to show the kinds of horrific abuses of power that could happen (and indeed, are likely to happen given human nature and corruptibility) if you had a super-secret organization that isn't accountable to few or no people and believes themselves to be "above the law". Despite most of these organizations being founded to protect ordinary people, at some point these organizations stop being protectors of the innocent and start being Illuminati-like shadow-dictators. The only reason the SCP Foundation isn't an outright villain is they are written as the lesser of two evils and from a narrative perspective they aren't allowed to be as corrupt as an organization like this probably would be in real life for plot reasons in order to maintain audience sympathy.

My question is, in a world where you have a secret or shadowy organization dedicated to containing the supernatural or weird, how could governments provide checks on them to prevent them from becoming a shadowy Illuminati-esque organization like the above? I.e., how do you keep nation-states and democratic governance relevant and keep the setting from devolving into NGO shadow wars like the SCP Foundation and similar settings are? Simply saying "well don't found such an organization and spread the duties out among several arms of government" wouldn't work because the trope is usually formulated around a single organization dedicated to handling supernatural occurences.

Specifically, what I'm thinking of is a governmental or inter-governmental organization founded to be the primary response and handler of supernatural occurrences (alien technology, magic, interdimensional weirdness), with at least some degree of secrecy, in order to keep the world mostly "normal" or keep dangerous anomalous technology or supernatural beings from interfering with humanity.

After doing research on the kinds of abuses the SCP Foundation and similar organizations get up to with their status, it dawned on me that it would be incredibly difficult for a governmental entity to actually keep them under control after a certain point, simply because the normal methods of bringing a rogue organization under control wouldn't work and it would be difficult to stop them from going full SCP Foundation.

• They can't really threaten to pull the organization's funding, as the organization often isn't dependent on government funding; they often fund themselves via selling applications of their technology, have some way of producing sellable goods with anomalous technology, or they are capable of buying shell companies or manipulating the stock market to fund themselves that way.
• The operatives of this organization have disproportionate power relative to their numbers. Most intelligence organizations cannot flaunt government control too openly because they don't have total control of the military and the military would win in a straight-up fight. This is not the case for one of these organizations, as they control most of the access to super-technology like spaceships, magic, laser-weaponry, and other force-multipliers that give them a huge advantage over the military, which relies more on conventional weaponry. This isn't even counting the secret government organizations whose members are all or in part wizards or superhumans. They also have access to a lot of doomsday weapons (engineered plagues, orbital weaponry) that conventional forces don't have.
• Many of these organizations are often depicted as having some sort of memory editing technology (neuralizers, amnestics, mind magic). Given this, governments would find it extremely difficult to maintain any sense of confidence that their decisions were their own. How do they know that they haven't had their memories altered or removed in order to better fulfill the shadowy organization's needs? Compared to IRL exampled of governmental tampering it is much more difficult to catch evidence of memory manipulation.

Given all this, it almost seems like the natural evolution of one of these organization would be one towards increasing corruption and totalitarianism simply because there's no one to hold these organizations accountable for anything. Self-policing and noble motivations sound good on paper, but human history has shown that without some kind of check and balances corruption rapidly runs rampant.

To be clear, I'm not asking about a plot-specific question as to how a dispute between the secret organization and the government would go. I'm asking about how to engineer a setting where the secret organization is accountable to higher authorities in some way and has to be concerned with consequences so that it cannot simply do whatever they want. I'm more thinking about a way in which an organization dedicated to police the supernatural can plausibly be kept a heroic and accountable protector of common humanity rather than shadowy unaccountable overlords.

Answer 1

Shhhh. They'll Hear You:

The simple answer is, you can't make an organization like this godlike without them having a god complex. Such an organization is only stable as a force of good if a.) deeply principled people are in charge, b.) They are dependent on existing legitimate organizations, c.) they have McGuffins that magically maintain "goodness" and d.) they feel compelled to maintain secrecy, thus maintaining the illusion of freedom for the general populous.

1. The best intended causes are only as good as those running it. Lenin proved to be less than perfect as the leader of communist Russia, but he still held to principles. But he chose to trust Joseph Stalin, of all people, as a worthy successor, because he was strong and ruthless. The same qualities that may make a person an effective leader may also be the qualities that make them someone you don't want with that kind of power.
2. If the organization is completely dependent on an existing legitimate organization, then it has some of that organization's stability. But this has two main flaws. The source organization will be corrupted by the need to maintain secrecy/eliminate transparency and use unspeakable power. Second, the secret organization also has a motive to remove the source organization's influence, either by finding alternate staff, funding, and authority. So you start with "good" CIA operatives, but you sometimes need to do things congress isn't okay with and is OBVIOUSLY too short-sighted to appreciate. You recruit foreign spies, possibly criminals, start using the McGuffin powers to manipulate the stock market or commodities market for flexible funds to maintain the vital work. And then they start doing the things that need to be done despite the government's orders. Now they are no longer dependent.
3. If you have a super-powered moral being like an AI or Dr. Manhattan from the Watchmen, your organization might stand a chance. The McGuffin itself should be something providing a moral compass like an angel (possibly literal) watching over the organization. Even here, as in the movie the Watchmen, this super-being only as perfect as those providing them intelligence.
4. Secrecy: If the organization is only able to do what it does in secret, then it has at least the motive to maintain the illusion of freedom. In the original Deus Ex, the Illuminati controlled the world, but no one knew about it - at least enough to prove. But majestic-12, a branch of the organization, seizes power and begins a campaign to conquer the world. One of the game solutions is to restore the Illuminati to power and let them reestablish control with the illusion of freedom. It's not perfect, but it is better than overt slavery.

So I'm not optimistic about your chances without a semi-divine being enforcing the rules to keep them honest. Power corrupts. Absolute power corrupts absolutely.

You could have progressively terrible solutions for the problem. If you held the members of the organization's families hostage at an undisclosed location, AND were willing to harm or kill those hostages, the organization would be held in check - until they found the location and freed their loved ones. Bombs built into the skulls of the organization members make them hostages. But these options get to be as terrible as the organization itself could be. So who is the evil, and who the victim?

Answer 2

Have Them Operate Out in the Open.

The best way to keep them accountable is by a lot of public scrutiny. The less people that know what’s going on the easier it is to get away with shady stuff.

Another option is to strip away the organization’s plot powers. Real organizations don’t have the manpower and resources to watch everything all at once. That gives the government agencies the chance to make moves against them.

Assuming options A and B aren’t available the governments can still go after the funding. Money doesn’t just appear. It should be relatively easy for the region equivalents of the IRS to notice the sheer amount of cash disappearing. The typical secret agency tends to operate on budgets that account for more then the whole worlds GDP.

The problem with using amassed WMDs is it only works until a crazy uses one. You may have apocalypse level weapons but so does the other side. And the fact that they haven’t already used one would indicate that they gain more from the world remain in a state of relative peace. Once you start a war it will go badly. Especially since they are severely outnumbered. Force multipliers can only go so far and once you break out the WMDs you will start losing ground, literally.