>who ran operations of the Deep State
The Deep State, strictly speaking, is largely just a mass of left leaning Washington DC fixtures whose entire lives (family, friends, etc) have come to depend on the bureaucracy. They 'resist' just out of some warped sense of patriotism and sense of govt's proper role in society.
Providing them gentle direction nudges and signalling are the politicians, MSM, and highly connected SES folks.
The SES folks take their direction from the permanent intelligensia, think tanks, senior politicians and their appointed department leaders.
Those take direction from the elite, via monetary and power handouts.
The CIA is just the secret police force to keep everyone in line. Bush was a cappo. Now Brennan.