I think you are purposefully ignoring facts, so that high level sentences match your narrative.
Flynn (security advisor for a couple of day) -- was setup.
There was no collusion with Russia to change 2016 election outcomes, that Flynn was accused of.
"... made materially false statements and
omissions during an interview with the Federal Bureau of Investigation ("FBI") on January 24,
2017, in Washington, D.C. "
[1]https://www.justice.gov/file/1015126/download
that's not collusion.
Roger Stone did not have his day in court, and the allegation were are not about directing Foreign powers to do anything.
Certainly hiring a foreign agent to write a document to be used trigger for FBI to initiate opposition party surveillances (like Clinton orchestrated) -- would have been a worthy avenue for Mueller to pursue, if he was about justice
The other indictments had nothing to do with 2016 election and happened for offenses outside 2016 election activities.
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In general, my definition of deep state is:
a shadow government (consisting of elected officials and hired bureaucrats), that performs illegal activities, but blames opposition exact same things they are guilty of.
Whether it is collusion with foreign powers to orchestrate a coup, or abuse of women, or anti-Semitism, or racism, launder money through charities, or get bribes for political favors.
The fact that left-wing media had zero interest in investigative reporting of the deep state, and the true collusions with foreign powers to orchestrate coup in this country --- in an indication of their actual profession (paid propagandists).