The author makes sure not to say anything too upsetting.

all governments—sometimes for good reasons—engage in concealment of their more questionable activities, or even resort to out and out deception

Considering that governments are supposed to act in our interest (because otherwise why would we accept them), and we're talking about governments doing something that we would find "questionable", i.e. against our interests (or plain immoral), what possible justification could there be for concealing it?

While an elected government might sometimes engage in activity that is legally questionable, there is normally some plausible pretext employed to cover up or explain the act.

Even smoking pot is "legally questionable" in many places, but that doesn't matter. The real question is whether something is immoral or not, and governments sure do lots of things that are immoral (taxation, for starters).

But if something immoral is done, a "plausible pretext" is just not good enough. In fact, nothing is, because nothing changes an act having been immoral at the time it was committed. Covering it up doesn't make it alright either.

This guy is just beating around the bush right from the start, where he framed the issue of a deep state in terms of a problem with the Turkish state in particular, as if there weren't one everywhere.

A deep state is basically just whatever group of elite innermost-insider psychopaths is actually calling the shots in a country. They operate behind the scenes of the public political circus, which is like a breeding ground for future members of the deep state. The most "accomplished" psychopaths are promoted, the rest keep competing for a spot (or being useful idiots).