WASHINGTON — The judge overseeing the case of President Trump’s former national security adviser Michael T. Flynn asked a full appeals court on Thursday to review an order by a panel of its judges to end the prosecution, saying their ruling marked “a dramatic break from precedent that threatens the orderly administration of justice.”
The request by the trial judge, Emmet G. Sullivan, was the latest turn in an extraordinary legal battle over the case against Mr. Flynn, who twice pleaded guilty to a charge of lying to the F.B.I. about his conversations with a Russian diplomat during the presidential transition in late 2016. The Justice Department sought in May to dismiss the case in a highly unusual move that prompted accusations of politicization, and Judge Sullivan appointed an outsider to argue against the department’s request rather than granting it.
Mr. Flynn’s lawyer, Sidney Powell, then asked the appeals panel to issue an emergency ruling over whether Judge Sullivan had the legal authority to scrutinize the Justice Department’s move. Last month, a divided panel ruled 2 to 1 in favor of Mr. Flynn, ordering Judge Sullivan to end the case without further review.
“The panel’s decision threatens to turn ordinary judicial process upside down,” a lawyer for Judge Sullivan wrote in the petition asking the full appeals court to examine the ruling. “It is the district court’s job to consider and rule on pending motions, even ones that seem straightforward.”
Mr. Flynn was the only White House official to plead guilty to a criminal charge in the Russia investigation. Judge Sullivan had been set to sentence Mr. Flynn in late 2018 but granted him more time to maximize his cooperation agreement and testify for the government against a former business associate in a foreign lobbying case.
But after Mr. Flynn hired new lawyers, he changed his stance, eventually declaring this year that he was innocent and seeking to withdraw his guilty plea. He made allegations of misconduct by prosecutors and the F.B.I., which Judge Sullivan rejected.
Attorney General William P. Barr stepped in, appointing the top federal prosecutor in St. Louis, Jeff Jensen, to review the case. As part of his review, Mr. Jensen handed over documents to Mr. Flynn’s lawyers, who declared them exculpatory.
That helped prompt the Justice Department to move to drop the case after a long public campaign by Mr. Trump and his allies, leading to accusations of political interference. None of the prosecutors who had worked on the case over the previous two and a half years signed the motion, and the lead prosecutor, Brandon L. Van Grack, withdrew from it altogether.
Instead of granting the motion, Judge Sullivan appointed a former federal judge and onetime mob prosecutor, John Gleeson, to argue against it and invited legal experts to weigh in, suggesting that he was skeptical of the government’s rationale.
Experts broadly disputed the Justice Department’s assertion that Mr. Flynn’s lies were not material since the F.B.I. was on the verge of closing its investigation of him, noting that they bore on the broader counterintelligence investigation into whether Trump campaign officials had coordinated with Russia’s 2016 election interference. Judge Sullivan had previously ruled that Mr. Flynn’s lies were relevant to the inquiry.
His decision to appoint Mr. Gleeson then spurred Ms. Powell’s emergency filing with the appeals panel seeking a so-called writ of mandamus, with the Justice Department arguing that if the case was not dropped it would harm the executive branch’s exclusive prosecutorial power.
The dissenting judge in the panel’s 2-to-1 decision said Mr. Sullivan should be allowed to rule.
“The district court must be given a reasonable opportunity to consider and hold a hearing on the government’s request to ensure that it is not clearly contrary to the public interest,” Robert L. Wilkins, a 2014 appointee of President Barack Obama, wrote.
The order had handed Mr. Flynn and the Justice Department a crucial victory as it meant that a hearing Judge Sullivan had scheduled for next week would not take place. The judge most likely would have pressed the Justice Department over its decision to drop the charge and why prosecutors who had worked at length on the case had not signed the motion.
In another development on Thursday, the Justice Department said it did not raise objections to Mr. Trump’s longtime friend Roger J. Stone Jr. beginning a 40-month prison sentence later this month. Mr. Stone had asked recently for a delay until Sept. 1 because of the coronavirus pandemic, citing health concerns, but a judge partly rejected his request, allowing him to put off the start of his sentence only until next week.
Mr. Stone was convicted of seven felonies in a bid to impede a congressional inquiry that threatened the president.
Another former aide to Mr. Trump, his onetime lawyer and fixer Michael D. Cohen, was taken back into federal custody on Thursday more than a month after being granted a medical furlough from prison, where he was serving a three-year sentence for campaign finance violations and other crimes.
The federal Bureau of Prisons said without elaborating that Mr. Cohen “refused the conditions of his home confinement.” A person briefed on his legal status said he had refused to sign papers agreeing to conditions related to media appearances and the writing of books.