In response to the Justice Department’s move to dismiss the case against former national security adviser Michael Flynn, U.S. District Judge Emmet G. Sullivan has taken some unusual steps. He first issued an order saying he will set a schedule for outside parties to file amicus (friend of the court) briefs concerning the legal issues presented by the government’s motion. He then appointed former federal judge John Gleeson to present the legal arguments opposing the motion and to advise Sullivan on whether Flynn should be held in contempt of court. Flynn’s lawyers and supporters are outraged that Sullivan won’t simply roll over and accept the Justice Department’s motion at face value. But given the extremely unusual, if not unprecedented, facts of this case, Sullivan’s actions are entirely appropriate.

Flynn pleaded guilty to lying to the FBI about his contacts with the Russian ambassador in December 2016 on behalf of the incoming Trump administration. He has actually pleaded guilty twice, before two different judges, admitting under oath that he knowingly lied to the FBI. Members of the Trump administration, including the president himself, agreed that Flynn lied, which is why he was fired after only a few weeks as national security adviser.

But Flynn later moved to withdraw his plea and have his case dismissed, based on alleged government misconduct. And, last week, in a remarkable motion, the Justice Department agreed with him. It argued that Flynn didn’t really lie, and that his conviction is flawed because the FBI had no legitimate reason to interview him in the first place. So after pursuing and defending Flynn’s prosecution for more than two years, the Justice Department is essentially saying, “Oops, never mind,” and asking Sullivan to dismiss the case.

Rule 48(a) of the Federal Rules of Criminal Procedure provides that the government may dismiss criminal charges “with leave of court.” Prior to a conviction, whether and how to proceed with criminal charges is a matter of prosecutorial discretion and the court usually should not interfere. As a former federal prosecutor, I’m the first to agree with that proposition. The court’s role is generally limited to ensuring that prosecutors are not harassing a defendant by, for example, repeatedly dropping and then refiling charges.

But what makes the Flynn case different, and so unusual, is that Flynn has already pleaded guilty. Once the court has gone through the solemn process of accepting a guilty plea, the balance of interests changes. Executive branch decisions about whether and how to prosecute are no longer implicated, because those decisions have already been made. The prosecution is largely over, the defendant stands convicted, and all that remains is sentencing — which is the prerogative of the judge. At that point, the court has a greater role to play in determining how the case proceeds.

The cases largely relied upon by Flynn and his supporters — including the most frequently cited, United States v. Fokker Services, B.V. — are cases involving prosecutorial decisions where there has been no guilty plea. That’s a crucial distinction. No one is pointing to cases in which the government has moved to completely drop a prosecution after a guilty plea because, frankly, no one can think of another example.

At the very least, because the government’s request is so unusual, it raises complex issues concerning how the court should proceed and what legal standards apply. With the Justice Department now in bed with Flynn, neither is going to present the other side of those issues to help Sullivan determine what to do next, and that makes it appropriate for a judge to invite outside experts to provide advice.

The court has institutional interests at stake here, as well. Judges have an interest in ensuring that parties, including the U.S. government, are not abusing the judicial process. Here, the government has abruptly switched sides and now disavows factual and legal arguments it made for two years. Given the ongoing concerns about Attorney General William P. Barr’s politicization of the Justice Department, the circumstances are suspicious. The judge is not required simply to serve as a rubber stamp and thereby become a possible accessory to prosecutorial misconduct.

It is likewise reasonable for Sullivan to explore holding Flynn in contempt. If Flynn now claims he didn’t lie to the FBI, it would mean he lied under oath to Sullivan during his plea. The judge can have no confidence that this Justice Department would pursue a perjury investigation, but he does have the inherent power to punish anyone who lies to him through contempt of court.

The fact that Sullivan is seeking a full airing of these issues does not indicate what he will ultimately do. He may well end up granting the government’s motion. Besides, if Flynn and his allies are correct that his prosecution was a miscarriage of justice, they should welcome a judge’s scrutiny. Perhaps it will showcase the FBI’s alleged misconduct and how Flynn was “set up” by a deep-state conspiracy. But the strident opposition by Flynn and his supporters to the court gathering more information suggests that they have something to hide. Let’s hope Judge Sullivan gets to the bottom of it.

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