Flynn made a lot of enemies in Washington.
His heart was always in the right place, but he was politically tone deaf, and naive.
In 2009 he wrote a paper for CNAS, with Cpt. Matt Pottinger, which argued that the intelligence community was doing a very poor job in Afghanistan and called for reform.
He described their work, and in fairness he was part of it, he was judging himself, as “marginally relevant.” It was harsh, but it was accurate. It’s also not something you should say if you want to hang around long.
He also support Robyn Gritz in her sexual harassment allegation against McCabe. And that was the right thing to do. But it earned him an enemy who could hurt him, and the effective ire of the FBI.
His greatest problem, was his opposition to the Obama administrations policy on terrorism, and Syria though.
He argued for an aggressive response to Isis. Which he didn’t get. The administration felt the threat was less serious and a lighter approach was sufficient.
In Syria he was concerned about that the growth of the jihadist movements, including AQ, who were fighting the Syrian government. Flynn did not support American aid for those jihadists, that aid was the centerpiece of the US plan to depose Assad.
The administration also felt they had won the war on terror, and to a degree, wanted to just declare victory. Flynn argued that the number of jihadists was actually exploding and that AQ still posed a serious threat to American security. Not only were we not winning, and we might even be losing. That wasn’t a message the administration wanted to embrace. And Flynn was not diplomatic.
Flynn also wanted to work more closely with Russia on terrorism and other security issues. That was considered dangerous talk. Most of the Russia specialists have Eastern European backgrounds, with roots in places like Poland, and view the Russia the way their forefathers did back in the old country. Peter Strozk and Col.Vindman are good examples of this. To them, working with Russia in any way shape or form, was unthinkable. And so Flynn got their attention.
So here you have man working for an administration that sees things very differently. And from their perspective, you have a man who is something of an annoyance. Clapper, Brennan, and Rice probably considered him disloyal by the end, for his inability to be quiet and get on board.
If they monitored him after he was fired, that was probably Brennan keeping tabs on him. Flynn was open and public about his continued disagreements with the administration.