"Cooperation only lasts as long as the status quo is unchanged."
--Patrick Gates (National Treasure)
A central objective of institutions is isomorphism, or sameness. Various processes that encourage institutional isomorphism may be mimetic, normative, and/or coercive in nature. These processes seek compliance and maintenance of the status quo.
An obvious problem with institutions is their maladaptive nature. Processes that promote sameness and compliance are of little use in turbulent environments that require innovation and change.
When facing such turbulence and threat of extinction, institutions have trouble responding with anything other than 'more of the same,' meaning that they intensify isomorphic processes in hopes of beating back the threat.
It should therefore be of no surprise that elements inside the federal government, such as the intelligence community, are rising up in defiance of Donald Trump. Being an outsider who has proposed radical change, Trump poses a significant threat to those in government institutions--particularly those under Trump's direct control, e.g., intelligence agencies. Even prior to his inauguration, Trump promised to restructure the national intelligence apparatus.
Because he has threatened the status quo, Trump should expect push back as the institution does the only thing that it knows how to do when facing an environmental threat.
Meanwhile, Judge Nap warns the president that there are intelligence elements inside of the executive branch that he will need to get rid of.
It seems likely that these agencies have not perceived such a threat to their existence since JFK. We know how that threat was terminated.