The JFK assassination is a good template to use when looking at the stuff.
No one agency knew what was happening.
It was a plot of individual people within agencies who worked together “off the books”.
Even the coverup is compartmentalized and most FBI agents working on it will be “just following orders” and will not know why they are doing what they are doing.
What you describe sounds like rogue elements within the agencies. It was probably a smaller group in Kennedy’s day.
I think they act more boldly, today, being larger in number, though still using compartmentalization to protect themselves. I am, for instance, willing to believe that the agents immediately around Trump were not, “in on it”. There was no reason for them to be.