Covert Group-While the intelligence agencies of the various powers may count as this, who really remains covert are the organizations that handle magical mistakes, Precursor artifacts that should never see the light of day, and any other mistakes of technology that could eat unfortunate innocent brains. How it’s handled really depends upon the nation involved. The Ministry of Ghosts is the Equestrian answer to this problem, a whole ministry (and the only ministry run by three alicorns) that operates covertly to deal with these problems before they become noticeable.
The Griffin Moot has the Special Working Group, which operates inside of the Imperial Intelligence Service (more Declare than the Equestrian Laundry), agents operating in a manner that short-circuits most conventional operations. And, they have to justify this to the ultimate masters of the Service and the Group when it happens. For the Senate and Minotaur Republic, this is Unit 999 that does some very…uncomfortable things when dealing with such technologies. For a nation that has a vicious paranoia about mental manipulation and mind alteration (even when voluntary), that Unit 999 can do what it does-and has the authority to do so-is an extremely worrying thing. The only justification that they can point to is the scale of the threat they face.
For the Zebras…what little is known in the structure of their nation is the enigmatic group only known as “the Silent Ones”. And, even this is believed to be an operational handle, not what the group is truly called.