Mike Segar / Reuters

There was an easy way for President Donald Trump to make the case against Michael Flynn go away.

The Constitution gives the president “Power to grant Reprieves and Pardons for Offenses against the United States,” and Trump hasn’t been shy about using the power in flamboyant ways. The man who pardoned Joe Arpaio while the criminal case against the former Maricopa County, Arizona, sheriff was still pending clearly has no compunction about cutting a case short using that power. The man who has dangled the possibility of pardons in cases arising out of the Russia investigation, including Flynn’s, doesn’t have scruples either about using it in matters that involve him directly. And Trump has made clear on numerous occasions that, at least in his view, Flynn deserves clemency; he has described him repeatedly as a good man destroyed by an investigation aimed at bringing down Trump himself.

A pardon would have been simple, wholly and unambiguously within Trump’s authority, and decisive, ending the case with a stroke of the presidential pen.

But Trump did not pardon Flynn. Instead, the president—or, rather, his attorney general—took a different approach. The Justice Department, under Attorney General William Barr, made an unusual request to the judge hearing Flynn’s case: The department sought to drop the prosecution, wiping away Flynn’s guilty plea. There has been no indication that Trump himself had any direct involvement in the decision, but he clearly approves of it. “Yesterday was a BIG day for Justice in the USA,” he tweeted after it was announced. “Congratulations to General Flynn, and many others. I do believe there is MUCH more to come! Dirty Cops and Crooked Politicians do not go well together!”

The move has been, to put it mildly, controversial. Plenty of good-faith critiques have been made by civil libertarians and defense attorneys about the federal government’s approach to criminal investigations and plea bargains. Those critiques do precious little to explain the Justice Department’s decision regarding Flynn. For one thing, the government’s brief requesting that the judge dismiss the case is laughably shoddy on almost every level. For another, it’s far from clear that there is any precedent for the federal government dropping a case against a defendant who has pleaded guilty without the government admitting to a violation of the defendant’s rights or newly discovered evidence of innocence.

The question is why Trump went this route, which has so far bought the department not a quick dismissal but a continuing headache. Rather than simply grant the government’s motion to dismiss, Judge Emmet G. Sullivan instead tapped a retired judge to present the case against dropping the prosecution—essentially requesting him to make the arguments that the Justice Department isn’t bothering to present. In response, Flynn’s legal team turned to the U.S. Court of Appeals for the D.C. Circuit, demanding that the appeals court order Sullivan to grant the government’s motion to dismiss. The appeals court has now asked the judge to explain his reluctance to scotch Flynn’s case, and invited the Justice Department to weigh in as well. Sullivan has retained counsel to represent him before the appeals court. And meanwhile, the prosecution remains on the books. Why buy all this trouble when a pardon was so easy?

We will not know the answer to this question unless and until the Trump White House papers become public. But Trump has clearly been quicker to threaten the use of pardons in cases that involve him directly than he has been to actually issue them. The reason, we suspect, is that the pardon—while an exceptionally powerful instrument—is imperfectly sculpted for the particular corrupt purpose that Trump is engaged in with respect to the Russia cases.

For one thing, a pardon makes the president personally accountable for the outcome. It quite literally takes place as a result of Trump’s personal signature. What’s more, pardoning Flynn does not really clear him of wrongdoing but, rather, overrules the judgment of his guilt by presidential fiat; the power of clemency, as Alexander Hamilton described it, is designed to serve as a granting of “exceptions” to the law, not a shaping of the law itself. As such, it does not validate any of Trump’s conspiracy theories about the Russia investigation: that the FBI was out to get Flynn from the beginning, that Flynn was railroaded as part of a “deep state” plot to bring down Trump. A pardon merely relieves Flynn of the consequences of his criminality.

By contrast, the Justice Department’s move to drop the prosecution—despite the legal mess it has created in the short term—has certain advantages. For one thing, the president’s hands are not on the matter. He can claim, perhaps even truthfully, that he left the whole thing to Barr, and that dropping the case was Barr’s call based on the supposed outrageousness of the investigation that led to it. Leave aside, for a moment, that anyone who has read any of the president’s tweets or listened to any of his rally speeches has heard him calling for this action. This is not merely a king’s plaintive pining for someone to rid him of a meddlesome priest. This is a king giving speech after speech and tweeting multiple times a day that the priest needs to be killed—and just in case that isn’t clear enough, emphasizing in each speech that by killed he means “dead.” But, that said, it’s perfectly possible that Trump never had a conversation with Barr in which he told him specifically how he wanted the case handled. Barr may well be able to say, quite honestly, that he’s never discussed the matter with the president—that this was his decision, not Trump’s.

In other words, doing it this way makes the outcome a product of the criminal-justice system, not an overruling of it. It makes this a reconsideration of the Flynn case by the apparatus of justice itself, not a jettisoning of the apparatus through the granting of “exceptions.”

And crucially, that apparatus includes the courts. The case, after all, cannot be dismissed without “leave of court.” And Sullivan’s insistence on hearing the matter briefed before granting his leave has triggered early recourse to the court of appeals. The result is that while Trump’s fingerprints on the matter are smudged, the Flynn case’s dismissal—if and when it comes—will bear the clear fingerprints of at least one, and maybe several, federal judges.

The cost of dispatching with Flynn’s case this way is high. However odious a pardon of Flynn would have been—and it would have been odious—the pardon power was designed, in part, to be a political tool. Hamilton suggested that a president might dispense mercy for utilitarian goals such as restoring “the tranquillity of the commonwealth” after an insurgency. To achieve the same result without using the pardon power, by contrast, the Trump administration has had to corrupt the justice system—which has political elements, to be sure, but is supposed to also administer justice impartially. It has had to misdescribe its own investigation. It has had to misdescribe the law. And it has had to whitewash the defendant’s conduct. And if the Justice Department now gets its way, the courts will, however reluctantly, have to give their imprimatur—their “leave,” in the language of the relevant rule—to Flynn’s good fortune.

There is something to be said for Sullivan’s refusal to snap to attention and play his assigned part in this charade. Yes, he may be forced to by higher judicial authority. And yes, he is testing the limits of his own power as a judge to supervise the inherently executive function of deciding whom to prosecute. But it was not Sullivan who invoked his jurisdiction here. It was the executive branch. And it was not Sullivan who wrote a rule that says the executive branch needs his permission before turning on a dime and dismissing a case against a man who has pleaded guilty, and admitted the relevant facts before the judge’s own eyes in response to his own questions.

It is not a crazy thing for a judge to take his time and hear some opposing arguments before acceding to a Justice Department brief that turns the facts of the case and the law on their head. And it is not a crazy thing for a judge to resist the Justice Department’s turning him into an instrument of presidential pardon by other means.

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