The other day I wrote in a comment:
My view is that what led the Deep State to regard Michael Flynn as "an existential threat," was the report he did at DIA which called out Obama for basically creating ISIS. The reason that posed an existential threat to the Deep State was because ISIS was part of a broader strategy. To have examined that more closely would have dragged in much, much more. So, despite his more or less conventional views in other areas, Flynn had to be neutered.
The same applies to Trump. Trump was too open to "revisionist" or "non-orthodox" foreign policy views that conflicted with the established Deep State policy. This is why he was perceived as such a threat. In fact, Trump's revisionism probably was viewed as running far deeper than Flynn's.
As things stand, I would rate Trump's success in furthering his views against the Deep State as only moderate to this point, largely because he's had his hands full fighting off Team Mueller and GOP Deep Staters.
Today Zerohedge has an interview - article that I highly recommend: How CIA & Allies Helped Jihadists In Syria: French Covert Ops Expert Exposes New Details. Here's the short intro that will give you the overview, but the article is rich in detail (some of which I'll include):
Maxime Chaix has written a shocker of a book in which he reveals insightful information on the support which several Western intelligence services provided to jihadist militias in Syria, starting with the CIA. His investigation reveals a multi-faceted state scandal and points out the murky game played by the Western powers and their Middle Eastern allies in the Levant.
So, in other words, at the heart of this book (La guerre de l’ombre en Syrie - The Shadow War in Syria) is the Clinton/Obama policy in the wake of the Iraq War and the "Arab Spring". That would be the policy that Flynn criticized when he was at DIA and whose criticism Trump adopted. Does that give you some idea of why the Deep State regarded both Flynn and Trump as "existential threats," and why the combination of the two in the White House increased that threat exponentially? Here's how the interview begins (but do yourself a favor and read the whole thing):
