WASHINGTON — The federal judge overseeing the case against President Trump’s former national security adviser Michael T. Flynn appointed a hard-charging former prosecutor and judge on Wednesday to oppose the Justice Department’s effort to drop the case and to explore a perjury charge against Mr. Flynn.
Judge Emmet G. Sullivan’s appointment of the former judge, John Gleeson, was an extraordinary move in a case with acute political overtones. Mr. Flynn pleaded guilty twice to lying to investigators as part of a larger inquiry into Russia’s interference in the 2016 election.
Mr. Flynn later began fighting the charge and sought to withdraw his guilty plea. Then last week, the Justice Department abruptly moved to drop the charge after a long campaign by Mr. Trump and his supporters, prompting accusations that Attorney General William P. Barr had undermined the rule of law and further politicized the department.
Judge Sullivan also asked Judge Gleeson to explore the possibility that by trying to withdraw his pleas, Mr. Flynn opened himself to perjury charges.
The Justice Department declined to comment. Judge Gleeson did not respond to a request for comment. Judge Sullivan had said on Tuesday that he would consider briefs from outsiders known as amicus curiae, or “friend of the court,” who opposed the government’s request to dismiss the case against Mr. Flynn.
While judges do sometimes appoint such third parties to represent an interest they feel is not being heard in a case, Judge Sullivan’s move was highly unusual, said Samuel Buell, a former federal prosecutor who now teaches criminal law at Duke University.
Judge Sullivan, he said, is essentially bringing in an outsider to represent the point of view of the original prosecutors, who believed Mr. Flynn had committed a crime before Mr. Barr intervened and essentially replaced them with a prosecutor willing to say he had not.
“This is extraordinary for the judge to appoint somebody to argue against a prosecutors’ motion to dismiss a criminal case,” Mr. Buell said. “But it’s extraordinary for a prosecutor to move to dismiss this sort of criminal case.”
“What the Justice Department did in the first case is, as far as any of us can figure out, unprecedented,” he added. “So the fact that this is pretty unprecedented too is not that surprising.”
It was not immediately clear what Judge Sullivan was focused on with his request for input on whether to essentially accuse Mr. Flynn of criminal perjury.
Mr. Buell said he doubted it would qualify as perjury for Mr. Flynn to embrace the Justice Department’s claim that he committed no crime because his admitted lies were purportedly immaterial to a proper investigation — whether or not that legal theory is true. But, Mr. Buell said, there could be a legitimate issue if Mr. Flynn were to claim that he did not lie after all — a notion the Justice Department’s filing also hinted at — despite previously telling judges that he had.
Mr. Flynn’s lawyers objected to Judge Sullivan’s earlier order suggesting he would accept input from third parties and said that outside opinions were best left to op-ed sections. “This court is not a forum for their alleged special interest,” Mr. Flynn’s lawyers wrote in court papers.
Judge Gleeson, who served on the federal bench in Brooklyn and ran the criminal division in the federal prosecutor’s office there, has already made plain his skepticism of the Justice Department’s motion to dismiss the Flynn case. He co-wrote an op-ed article this week in The Washington Post urging Judge Sullivan to scrutinize it.
“Prosecutors deserve a ‘presumption of regularity’ — the benefit of the doubt that they are acting honestly and following the rules,” he wrote along with two other former federal law enforcement officials in New York. “But when the facts suggest they have abused their power, that presumption fades.”
The department made conflicting statements to the court, they wrote, saying that Judge Sullivan had the “authority, the tools and the obligation” to decide whether the motion to withdraw was credible.
“There has been nothing regular about the department’s effort to dismiss the Flynn case,” they wrote. “The record reeks of improper political influence.”
The son of Irish immigrants, Judge Gleeson has said in interviews that he took a job as a prosecutor in Brooklyn after he was rejected from a post in the Manhattan federal prosecutor’s office, then run by Rudolph W. Giuliani.
As a prosecutor in Brooklyn, Judge Gleeson rose to legal stardom when he successfully prosecuted the notorious mobster John Gotti. President Bill Clinton appointed him to the federal bench in 1994, and he served until 2016.
Judge Gleeson is highly regarded among current and former prosecutors who described his sharp courtroom skills in putting mafiosos and other criminals in jail. But he also fought for lower sentencing guidelines and advocated on behalf of policies that would keep nonviolent offenders out of prison.
“Judge Gleeson brings a keen sense of justice and of federal court procedures to the task of seeking to understand how this very unusual case came about,” said Carl Tobias, a professor at the University of Richmond School of Law.
He shares that sense with Judge Sullivan, who has displayed little tolerance for the government overstepping its bounds. After prosecutors secured a conviction on corruption charges in the 2008 trial of Senator Ted Stevens of Alaska, Judge Sullivan dismissed the charges and ordered an independent prosecutor to examine whether the prosecutors had improperly withheld evidence.
“In nearly 25 years on the bench,” he said in an angry lecture, “I’ve never seen anything approaching the mishandling and misconduct that I’ve seen in this case.” A report later backed his suspicions, but no charges were filed.
Judge Sullivan, a Clinton appointee as well, has also closely overseen Mr. Flynn’s case since he began presiding over it in 2018. He noted at an aborted sentencing hearing that year that he was alarmed to see Mr. Flynn appear to argue in court filings that he had not really lied and that investigators had coerced him.
Judge Sullivan demanded that Mr. Flynn acknowledge he had entered his plea “knowingly, voluntarily, intelligently, and with fulsome and satisfactory advice of counsel.” He said he could not remember accepting a guilty plea “from someone who maintained that he was not guilty, and I don’t intend to start today.”
He also excoriated Mr. Flynn for his crime, noting that he lied to federal agents on the grounds of the White House. “I can’t make any guarantees, but I’m not hiding my disgust, my disdain for this criminal offense,” the judge said.
Internal tensions over the Justice Department’s decision to withdraw the charge against Mr. Flynn have also seeped into view. The career prosecutors on the case squared off against other law enforcement officials, including the U.S. attorney in St. Louis, Jeff Jensen, whom Mr. Barr brought in to review it, according to people familiar with the conversations.
They argued about whether the fact that Mr. Flynn had lied to investigators about communications with the Russian ambassador to the United States at the time, Sergey I. Kislyak, was material to the department’s larger investigation into Russian election interference. In seeking to dismiss the charge, the department insisted it did not.
Additionally, Bill Priestap, the former head of F.B.I. counterintelligence, cast doubt on their argument for dropping the case in an interview conducted just days before the department filed its motion.
The department did not include information from Mr. Priestap’s interview when they told the court they wanted to dismiss the case. A Justice Department official said that law enforcement officials were writing a report on the interview and would soon file it with the court.
Judge Sullivan’s unusual appointment of Judge Gleeson came after another federal judge in Washington criticized Mr. Barr’s handling of the Russia investigation. In a ruling in a separate a Freedom of Information Act lawsuit, Judge Reggie B. Walton said that Mr. Barr presented a “distorted” and “misleading” picture of the report by the special counsel, Robert S. Mueller III, before he made it public.
Judge Walton questioned whether Mr. Barr “made a calculated attempt to influence public discourse about the Mueller report in favor of President Trump.”
Charlie Savage, Adam Goldman and Michael Crowley contributed reporting.