For more than three years, Michael Flynn waged a strange battle to clear his name after pleading guilty to lying to FBI agents and then declining a judge’s invitation to withdraw the plea. But there has always been something very wrong about the case, and we’ve learned more about it in recent weeks.

The retired army general, fleetingly President Trump’s first national-security adviser, was investigated during the Trump transition by anti-Trump officials at the FBI and Obama Justice Department on nebulous grounds.

There was no criminal predicate for the probe: Flynn’s communications with Sergey Kislyak — then the Russian ambassador to the U.S. — during the transition, which set off the whole affair, were entirely proper. The idea that they violated the Logan Act forbidding private interference in the conduct of U.S. foreign policy was always absurd. The last indictment under the constitutionally dubious act was in 1852, and the statute wasn’t meant to tie the hands of high-level officials of an incoming administration.

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Former FBI director James Comey broke protocol by having agents interview Flynn at the White House on his first day on the job, a tactic Comey subsequently told a chortling New York City audience he wouldn’t have been “gotten away with” in a more organized administration. Though the agents had a recording of his conversation with the ambassador, they didn’t play it for Flynn — instead simply grilling him.

The just-revealed notes of an FBI official prior to the interview ask whether the goal was to elicit Flynn’s admission that he talked with Kislyak about sanctions (the supposed Logan Act violation) or “to get him to lie, so we can prosecute him or get him fired.” The notes are open to interpretation, but it’s not clear what the FBI was doing besides hoping he’d lie.

In a newly disclosed email, Lisa Page suggests slipping in as unobtrusively as possible a warning that lying to the FBI is a crime, so as not to put Flynn on his guard.

Still, the agents who interviewed Flynn didn’t think he lied. Even if he did, as our own Andrew C. McCarthy has noted, a false statement is not supposed to be actionable unless it is material to something properly under investigation.

This paper-thin case (at best) was apparently on the verge of being closed when top FBI officials intervened to keep that from happening. Then, the case got picked up by Special Counsel Mueller’s team. Mueller’s prosecutors pressured Flynn to plead guilty, hoping he’d help make some sort of case against Trump.

That obviously came to nothing, but Flynn has been financially ruined and still faces jail time.

As for Flynn’s guilty plea, his counsel contends that new disclosures show it was elicited on the basis of threatening his son with prosecution. His son’s alleged crime was failing to register with the Justice Department as a foreign agent. Such a violation of the Foreign Agents Registration Act had almost never been charged by the Justice department prior to Mueller’s investigation, and it’s not even clear the act would apply to Flynn’s son.

None of this was revealed to the court until now.

It was highly convenient for the Mueller team to have the Flynn guilty plea as a high-profile scalp to wave around for the media, which did indeed take delight in it and use it to argue that the probe was “closing in on” Trump.

We were never fans of Michael Flynn’s appointment as national-security adviser. How he handled himself in this matter — and especially his work for the government of Turkey while advising Trump in 2016 — shows poor judgment. But he’s been treated unjustly.

The court, Attorney General Bill Barr, and President Trump should all consider remedies. This isn’t how our justice system, or high politics, should work.