WASHINGTON — A federal appeals court in Washington appeared inclined Tuesday to let a judge decide on his own whether to grant the Justice Department’s request to dismiss the criminal case against former Trump administration national security adviser Michael Flynn.

Michael Flynn

Members of a federal appeals court expressed skepticism on Tuesday of arguments that a judge was not empowered to probe the motives behind the government’s decision to abandon the prosecution of former National Security Adviser Michael Flynn, shown in 2017. Carolyn Kaster/Associated Press

The court expressed skepticism at arguments from the Justice Department and Flynn’s attorneys that a judge was not empowered to probe the motives behind the government’s decision to abandon the prosecution of Flynn, who pleaded guilty to lying to the FBI as part of the special counsel’s investigation into the Trump campaign and Russia.

The more than three hours of arguments were the latest step in a long-running legal saga that has prompted an extraordinary power struggle between the executive and judicial branches. The case will almost certainly persist for months if the court rejects Flynn’s efforts to get a speedy dismissal and returns it to U.S. District Judge Emmet Sullivan, who refused to immediately grant the department’s request to drop the prosecution.

The court is not deciding whether the case should be dismissed or whether the Justice Department had good reason to move to drop it in May despite Flynn’s own guilty plea. Instead, the question before the court is a more procedural one: whether Flynn’s attorney is entitled to leapfrog Sullivan and get an order from the appeals court forcing him to dismiss the prosecution before Sullivan himself has had the chance to rule.

A ruling against Flynn would not undo his guilty plea or end the case but simply return it to Sullivan for a hearing on the government’s request to dismiss.

The entire court took up the matter after a three-judge panel, in a 2-1 ruling, ordered Sullivan to dismiss the case. Several of the judges made clear through their questioning that they were deeply skeptical of arguments that Sullivan was not entitled to scrutinize the department’s decision and second-guess the motives behind it.

Judge Thomas Griffith, an appointee of President George W. Bush, bristled when Flynn’s lawyer, Sidney Powell, characterized as “pretty ministerial” the role of a judge when the government and the defendant both agree that a case should be dismissed.

“It’s not ministerial and you know it’s not,” Griffith said. “So it’s not ministerial, so that means the judge has to do some thinking about it, right?”

Judge Cornelia Pillard, an appointee of President Barack Obama, said that though the Justice Department is entitled to deference, “the integrity and the independence of the court” must also be respected.

She told Jeffrey Wall, the acting solicitor general, that by urging Sullivan to dismiss the case, it was asking him to contradict an order he had already given when he accepted Flynn’s guilty plea nearly two years ago.

“What self-respecting Article III judge would simply jump and enter an order without doing what he could to understand both sides?” Pillard asked, referring to the section of the Constitution that created the judiciary branch.

Flynn was the only White House official charged in special counsel Robert Mueller’s Russia investigation. He pleaded guilty to lying to the FBI about having discussed sanctions during the presidential transition period with the then-Russian ambassador to the United States. Those concerns prompted alarm within the FBI because White House officials had stating publicly that Flynn and the ambassador had not discussed sanctions.

Flynn was awaiting sentencing when the Justice Department announced in May that it was abandoning the case following an internal review. That review concluded that the FBI had insufficient basis to question Flynn about his conversations with the diplomat, which Attorney General William Barr says were appropriate,

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