Why is the government seeking to drop charges against Michael Flynn even though he pleaded guilty — in two admissions in court — to committing the crime at issue?

The short answers: The Justice Department is giving him a break. And Flynn has played his cards well.

The long answer: It’s a long story.

The deal

Flynn admitted to lying to the FBI about conversations he had had with Russia’s then-ambassador to the United States as he and the rest of President-elect Donald Trump’s camp waited in the wings early in 2017.

That case appeared clear. But the former Army lieutenant general also had been involved with other enterprises that might have resulted in more charges — including undisclosed foreign lobbying — and his deal with prosecutors swept that off the table.

It also apparently avoided prospective charges for Flynn’s son. Flynn and his attorneys considered the deal to be the least bad way out of the jam.

“My guilty plea and agreement to cooperate with the special counsel’s office reflect a decision I made in the best interests of my family and of our country. I accept full responsibility for my actions,” Flynn said in late 2017 at the time of his plea.

All the same, few knew at the time of that submission how problematic Flynn’s fateful interview with the FBI would be for nearly everyone else involved, including the specific FBI agents, the leadership of the bureau and the Justice Department.

The conversation

Former FBI Director James Comey since has described the question about whether Flynn had lied, or whether to charge him, as “a close one.”

U.S. Attorney Timothy Shea quoted that statement in his brief about the Flynn case filed Thursday to seek the dismissal of the charges, along with the notes of the FBI agents that also have since come to light.

In those materials, the investigators appear to wonder what they’re doing preparing to interview Flynn.

“What is our goal — truth, admission or to get him to lie so we can prosecute him or get him fired?” one note read. Another says: “[White House] will be furious” and “protect our institution by not playing games.”

Flynn’s attorneys fought to get this material unsealed after their dealings with the government soured. They call it the basis for their claim that the FBI effectively entrapped him.

The Justice Department’s new brief cites these materials and argues that the bureau had all but concluded that Flynn wasn’t a counterintelligence risk as it was looking into prospective links between Trump’s camp and the Russian interference in the 2016 election.

In this new reasoning, Flynn’s false statements to investigators weren’t ‘”material’ to any bona fide investigation,” Shea wrote — so the case shouldn’t continue.

What about the guilty pleas?

Attorney General William Barr was clear in an interview with CBS News on Thursday evening: “People sometimes plead to things that turn out not to be crimes, and the Department of Justice is not persuaded that this was material to any legitimate counterintelligence investigation. So it was not a crime.”

Change in the weather

Also unknown to the public at the time of Flynn’s interview were the disputes about it taking place within and between the FBI and the Justice Department.

The procedures — or lack thereof — that were followed then helped create the opening for the new legal interpretation by Barr that the Flynn case was improper.

Comey’s fingerprints and those of other former bureau leaders were all over the decisions made about what to do and whom to tell and not tell about Flynn’s interview. Those names are now mud with most Republicans, and that, separate from the legal interpretations, make the politics safe within the GOP for Trump and Barr to let Flynn go.

Democrats argue that Trump and Barr have made a mockery of what was intended to be an independent Justice Department, first with the intercession in the sentencing of Trump’s friend Roger Stone and now with Flynn.

The player

Through all this, Flynn and his attorneys sought the best deal they could get at each juncture. First, they turned state’s evidence.

Intitially, prosecutors called him a model cooperator and told a judge they would be fine if he received a sentence of only probation, even though federal guidelines contemplated at least a few months in prison.

The longer Flynn cooperated, however, the more fraught became his relationship with the feds. After giving prosecutors everything they wanted in the Russia matter, Flynn became less forthcoming when the government brought a case against his former business partner, prosecutors said.

The U.S. Attorney’s Office for Washington D.C., which took the prosecutorial baton from special counsel Robert Mueller’s office, told a judge that it thought Flynn should be sentenced to as many as six months.

That could include probation, it said — but didn’t rule out the prospect of prison time, given how much less helpful prosecutors said Flynn had become.

By this point, in mid-2019, Flynn had changed out his legal team, and it howled at the prospect of prison after all the work he had done for the Justice Department.

That “stunning and vindictive reversal,” as Flynn’s lawyers called it, was one basis for their request to withdraw the guilty plea earlier this year, notwithstanding Flynn’s admission of guilt and months of cooperation.

It also fueled their quest to obtain more of the core documents about Flynn’s interview, which revealed the notes from the FBI investigators.

The sentencing that wasn’t

In a strange twist, what might have set the stage for Flynn’s eventual release was an encounter with an outspoken judge who raised the prospect of punishing him more severely.

Nearly everyone, including Trump, expected Flynn to be sentenced in late 2018 when he appeared before Judge Emmet Sullivan in Washington. Flynn and prosecutors invited family members to be with them in court.

But the judge yielded surprises and headlines with his spirited remarks about the case.

“I’m not hiding my disgust, my disdain, for this criminal offense,” he said.

Sullivan asked prosecutors whether Flynn might have committed “treason,” raising the prospect that Flynn might get prison time after all. No, the government said, it didn’t consider that part of the case.

Ultimately, Sullivan deferred the sentencing because he said he had more questions about the matter, adding more months to Flynn’s legal saga.

If Sullivan had issued a sentence then and resolved Flynn’s case, Flynn’s admissions and guilt might have stood. His legal odyssey might have ended there.

Instead, the judge’s delay led to the phase of the story in which Flynn replaced his attorneys and broke with the government. His new legal team fought for and obtained the FBI memos and sought to rescind the guilty plea.

That dispute was still ongoing when the Justice Department decided this week to drop the case. In the end, Flynn and his lawyers outlasted everyone.