In Terry Hayes' excellent and scary thriller "I Am Pilgrim", the hero works for a super-secret and totally deniable organisation called 'The Department'. Basically it audits the spies - with few restrictions on what it can do.
In China Miéville's wonderful "The City and the City" there's a super-secret organisation called Breach which has almost unlimited power in its bizarre domain.
Operatives of these super-secret organisations have a problem, it seems to me. Probably no-one has heard of their secret organisation, nor are they permitted to identify themselves with it.
So how then do they gain authority to interview people, task military/police assets and generally grab the logistical resources they need?
Semi-spoiler: I'm still wondering how easy it would be to create from scratch a synthetic version of a deadly virus. Once fabricated, the deployment mechanism in "I Am Pilgrim" seems horribly plausible.