The United States Intelligence Community (USIC) is comprised of 16 agencies/entities which in turn fall under the general auspices of the Office of the Director of National Intelligence (ODNI). The ODNI and its head DNI, were created as a response to 9/11 and wrested control of the IC from the CIA effectively, but not really. This occurred under Bush but was never consolidated. The DNI reports to POTUS and had been so throughout the last administration. In addition, this ODNI had access to additional strategic intelligence which worked its way up through the top of other agencies, not already under control of the Deep State (DS). I'll spare everyone the big long list. Yeah, Wikileaks sucks but all of the information is more or less accurate in this overview: https://en.wikipedia.org/wiki/United_States_Intelligence_Community

There is no unified "military intelligence" per se. Each service branch has its own "military intelligence" entity. Military intelligence agencies, of course, cooperate with the Defense Intelligence Agency (DIA). The DIA exists to collect intelligence for military-related purposes. That definition, can be applied broadly.

About Flynn: (Wikipedia) "In September 2011, Flynn was promoted to Lieutenant General and assigned as assistant director of national intelligence in the Office of the Director of National Intelligence.

On April 17, 2012, President Barack Obama nominated Flynn to be the 18th director of the Defense Intelligence Agency.[21][22] Flynn took command of the DIA in July 2012.[23]

He simultaneously became commander of the Joint Functional Component Command for Intelligence, Surveillance and Reconnaissance, and chair of the Military Intelligence Board." Flynn was also very tied into another entity you should be aware of, US Army INSCOM - United States Army Intelligence and Security Command. These are 10,000+ active, GS, and civilian personnel who have a wide-range of find, fix, and finish solutions, in conjunction with more conventional military and intelligence roles. INSCOM has very close ties with the NSA, which is still a military and not civilian agency, like the CIA.

What is generally not discussed is Flynn's former command of...."Military Intelligence" - Flynn was for Joint Special Operations Command (JSOC) aka DEVGRU (Seal Team 6), Combat Applications Group (CAG)(aka Delta Force) and a handful of other special operations groups commonly referred to as "tip of the spear". These operators and their REMFs ((;)) are largely incorruptible absolute patriots in the truest sense of the word. /most "operators" are never truly out, because they never want to leave. That bond extends all the way to the men who led them - Flynn, McChrystal, and others had the keys to the Ferrari (JSOC) and they test drove it thoroughly. The last administration could not crack the top of JSOC. So those motherfuckers...Extortion 17 is all I have to say.

So, if you were Trump and wanted a group of highly motivated and revenge-minded individuals who stared the Deep State in the mouth and tried to kill it, spilling only their own blood, to exact revenge, who would it be? Fucking JSOC is who I'd pick - Vegas was the first preview. (Mr. Prince hopefully is getting his hands dirty as well)

So under what circumstance would this occur? That, I'd love to know. But I'm pretty sure some form of legally enforceable, light footprint martial law would trigger that. This would allow POTUS to take direct control of any assets he deems necessary - INSCOM runs ops, JSOC performs takedowns and special mission taskings, USMC (look who surrounds POTUS) (possibly in some clause in the USMC charter?) would allow POTUS to use the Marines to oversee the National Guard elements? Though NG units are under control of the state governors. So I'm not clear in this area. Any JAGs in the room?