Flynn was part of it but not all of it. They hated Trump.
MICHAEL LEDEEN:
“…What, then, was it all about? I think I know. It was all about General Flynn. I think it began on the battlefields of Iraq and Afghanistan, when Flynn changed the way we did intelligence against the likes of Zarqawi, bin Laden, the Taliban, and their allies.
General Flynn saw that our battlefield intelligence was too slow. We collected information from the Middle East and sent it back to Washington, where men with stars on their shoulders and others at the civilian intel agencies chewed it over, decided what to do, and sent instructions back to the war zone. By the time all that happened, the battlefield had changed. Flynn short-circuited this cumbersome bureaucratic procedure and moved the whole enterprise to the war itself. The new methods were light years faster. Intel went to local analysts, new actions were ordered from men on the battlefield (Flynn famously didn’t care about rank or status) and the war shifted in our favor.
This earned him a following among some who worked for or with him, but it also gained him the enmity of those who had been cut out of “the chain of command.” By the time he was made head of DIA, Flynn had a real problem with the intelligence community, first because he had marginalized them, and for another reason: Flynn was determined to do a full-scale analysis of the (many) secret missions that had not been carried out over the years, and he wanted an accounting of the considerable funds allocated for them.
So there were many high-ranking intelligence officials who were out to get Flynn. You can see them at work long before there was a hint of Russiagate, when the target was not yet Donald Trump. But then things got worse for the IC, when Flynn was named to head DIA. By then, the FBI was fully engaged in the anti-Flynn campaign, paying people like Stefan Halper to surveil Flynn’s behavior in Great Britain. This produced the fanciful accusation (impossible, for anyone who knew the general) that Flynn had flirted with a good-looking Russian historian. This may have been the start of the “collusion” allegations…”