After Attorney General Bill Barr’s Justice Department announced last week that it’s dropping the charges against former foreign agent Michael Flynn, Donald Trump celebrated his former advisor’s “total exoneration.” The presidential comments were clearly foolish at the time.

But as the process progresses, Trump’s boast is starting to look a little worse. On Tuesday, the federal judge overseeing the case, Emmet Sullivan, said in a filing that he’ll allow outside parties to weigh in on Flynn’s case, opening the door to possibly rejecting the Justice Department’s motion to dismiss the pending criminal charges. Yesterday, the same judge went a little further.

The federal judge overseeing the case against Ret. Lt. Gen. Michael Flynn has appointed a retired judge to present arguments in the case opposing the Department of Justice’s request to dismiss the charges against the ex-national security adviser. Judge Emmet Sullivan said that he wants retired Judge John Gleeson to present those arguments about why the charges against Flynn shouldn’t be dropped and to explore the possibility that Flynn lied to Sullivan.

NBC News’ report added that Sullivan expects Gleeson to consider whether Flynn, who’s already pleaded guilty twice, could be held in criminal contempt for perjury.

This isn’t what the attorney general had in mind for the president’s disgraced former ally, but it’s not up to Barr to dictate orders to the federal judiciary.

If John Gleeson’s name sounds at all familiar, there’s a good reason for that. It was just a few days ago when Gleeson — who served as a U.S. district judge for the Eastern District of New York and chief of the Criminal Division in the U.S. Attorney’s Office in that district — co-authored a Washington Post op-ed on the Flynn case. It read in part, “There has been nothing regular about the department’s effort to dismiss the Flynn case. The record reeks of improper political influence.”

The fact that Sullivan tapped Gleeson to present arguments in the case should probably make Flynn, his defense counsel, and political players trying to pull strings on Flynn’s behalf a little nervous.

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Making matters slightly worse, Mary McCord, the former acting assistant attorney general for national security at the Department of Justice, has accused Barr’s Justice Department of “twisting” her words in the Flynn case. As the New York Times reported, she’s not the only one with concerns.

A key former F.B.I. official cast doubt on the Justice Department’s case for dropping a criminal charge against President Trump’s former national security adviser Michael T. Flynn during an interview with investigators last week, according to people familiar with the investigation. Department officials reviewing the Flynn case interviewed Bill Priestap, the former head of F.B.I. counterintelligence, two days before making their extraordinary request to drop the case to Judge Emmet G. Sullivan. They did not tell Judge Sullivan about Mr. Priestap’s interview.

According to the reporting, Priestap’s notes about the FBI’s questioning of Flynn in 2017 were used to suggest the bureau was trying to entrap Flynn. The Times added, “That interpretation was wrong, Mr. Priestap told the prosecutors reviewing the case. He said that F.B.I. officials were trying to do the right thing in questioning Mr. Flynn and that he knew of no effort to set him up. Media reports about his notes misconstrued them, he said, according to the people familiar with the investigation.”

When the Justice Department said last week that it could not prove Flynn is guilty of the crimes to which he’s already pleaded guilty, it appeared the former White House national security advisor was effectively in the clear. Seven days later, that no longer appears to be the case.

Postscript: Some prominent Fox News personalities last night turned their rhetorical fire on Judge Sullivan, which I suppose was to be expected. To the extent that this matters, it was Ronald Reagan who first made Sullivan a D.C. judge, and it was George H.W. Bush who elevated Sullivan to the D.C. Court of Appeals eight years later. Bill Clinton chose Sullivan for the federal bench in 1994.