I’m not sure I buy the headline of Mike Ledeen’s article; 
Make No Mistake: The Mueller Investigation Was All About Flynn
As a matter of fact the headline seems to go well beyond the scope of the article itself.
That said, however, it seems to me he raises an interesting point when he suggests is that the attempted throttling of Flynn was the genesis of the idea of what eventually became the Mueller investigation.
Flynn was never popular with the intelligence community because of the way he routinely bypassed them. His reasoning was certainly simple enough… being the same reason that anyone would bypass a bureaucracy… slow, unresponsive, and usually coming up with the wrong answers.
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.
After Flynn was driven out of his post at DIA, things got even more threatening to the intelligence officials, as he became a prime advisor to candidate Trump and, early in the campaign, other Republicans. After the 2016 elections, the IC officials went all-out to keep him out of the White House, sometimes resorting to spreading ridiculous stories. President Obama warned Trump not to appoint Flynn as national security advisor, and Susan Rice actually warned the president-elect that Flynn might be in violation of the Logan Act, for which nobody has ever been prosecuted, and hence blackmailable by the Russians. Meanwhile, the Bureau had opened a counterintelligence investigation of Flynn’s activities. His digital communications were monitored, “unmasked” at the request of Obama officials, and leaked to friendly journalists.
The operation against Flynn provided the model for the anti-Trump assault. When the “collusion with Russia” allegations drove Flynn out of office, the intel officials realized the same methods could prevail against the president. That effort has apparently ended with Mueller’s rejection of the “collusion” allegations.
This is actually a fairly reasonable surmise.. and from it Ledeen has a wonderful suggestion:
The accusations against Flynn were fanciful from the outset, and need to be undone. If justice is to prevail for this distinguished officer, he should be pardoned at once, and then the president has the opportunity for a positive step: create a high-powered commission to investigate the many sins of the intelligence community. Flynn’s plan to audit their budgets—no such appraisal has been carried out since World War II—was worthy and important. The president should make General Flynn the chair of that committee, to restore his good name and give intelligence the kind of serious evaluation we badly need.
I fully agree that this is something the President should seriously consider.