In pausing the Justice Department’s efforts to reverse the guilty plea of former Trump aide Michael Flynn, U.S. District Judge Emmet G. Sullivan this week bolstered a reputation built over 36 years as one of the department’s most probing skeptics on the federal bench.

Sullivan on Wednesday appointed former federal judge John Gleeson to oppose the department’s request to abandon its two-year-long prosecution and exonerate the former national security adviser. Sullivan also asked Gleeson to examine whether Flynn may have committed perjury by admitting, under oath in December 2017, to lying to the FBI about his Russian contacts and later claiming innocence.

Sullivan’s extraordinary action recalled to many his excavation of one of the Justice Department’s worst scandals a decade ago — the botching of a campaign finance investigation into Sen. Ted Stevens (R-Alaska).

Sullivan’s work then won plaudits from former prosecutors and fierce critics of government tactics alike. After overturning Stevens’s 2009 conviction of lying on disclosure forms, the judge named a special prosecutor who found that at least two federal prosecutors withheld evidence that would have acquitted the nation’s then-longest-serving senator. A third prosecutor died by suicide before the report was completed.

“Judge Emmet Sullivan, to all those who seek, hallow, and do Justice. With the greatest respect and gratitude for your honorable service,” one former U.S. prosecutor and white-collar defense appeals specialist wrote to Sullivan in April 2014.

The writer was Sidney Powell, Flynn’s current defense attorney. She wrote the tribute when signing and sending Sullivan a copy of her book, “Licensed to Lie: Exposing Corruption in the Department of Justice,” the judge recalled in court when she joined Flynn’s case in June. The book alleged misconduct by prosecutors investigating the 2001 collapse of the Houston energy company Enron.

To lawyers who practice before him and judicial colleagues who work alongside him, Sullivan’s intolerance for official misconduct is a defining characteristic, backed by his plain talk and comfort in the spotlight.

“Judge Sullivan usually gives prosecutors a hard time, not because they’ve necessarily done anything wrong but because he holds the government to a very high standard,” Glenn Kirschner, a former federal prosecutor who has often appeared before Sullivan, said in 2018.

That instinct has played out to Flynn’s disadvantage at times, he said.

“And why?” Kirschner said. “The defendant was a high-ranking government official” who admitted to egregious conduct, he said.

Sullivan, 72, is no stranger to Washington controversies. The D.C.-born son of a police officer is a graduate of Howard University School of Law and the longest-serving active federal judge on the U.S. District Court for the District of Columbia.

He was appointed in 1994 by President Bill Clinton after earlier being named by President Ronald Reagan to the D.C. Superior Court and President George H.W. Bush to the D.C. Court of Appeals.

After his start at Houston and Gardner, a storied Washington civil rights law firm that has produced a string of judges, Sullivan became a pillar of the city’s judicial system. He has played a longtime role on panels overseeing and nominating D.C. judges and coordinating oversight of the District’s sometimes-troubled jail system.

He also has been named by former Supreme Court chief justice William H. Rehnquist and current Chief Justice John G. Roberts Jr. to oversight roles for the federal judiciary, including to its committee on criminal law from 1998 to 2005.

In 2016, Sullivan roiled the political waters when he criticized Democratic presidential candidate Hillary Clinton’s use of a private email address while secretary of state, at one point during a public records lawsuit decrying the “drip, drip, drip” of revelations about her email use. “When does it stop?” he said.

In overseeing the Flynn case, Sullivan finds himself in one of the most tangled thickets yet. Flynn was the first and only former Trump administration aide to plead guilty and cooperate with special counsel Robert S. Mueller III’s Russia investigation. But after Mueller closed shop last year, the foreign policy adviser reversed course. Flynn began seeking to void his guilty plea to lying about his contacts with Russia’s ambassador related to easing U.S. sanctions and about his undisclosed lobbying work for Turkey before President Trump took office.

The Justice Department fought Flynn’s attempts until April 30, when a review ordered by Attorney General William P. Barr said Flynn should never have been interviewed in the FBI investigation and therefore any of his lies were immaterial.

Sullivan has a reputation as a leading judicial advocate for fuller disclosure of evidence by prosecutors to defendants. But so far he has balked at Flynn’s argument that he was entrapped. In twice having Flynn admit his guilt in court under oath, Sullivan in 2018 said he did not recall ever taking “a plea of guilty from someone who maintained that he was not guilty, and I don’t intend to start today.” Sullivan also explicitly said to Flynn “that any false answers will get you in more trouble.”

Powell has advocated fiercely for Flynn since taking on the former three-star Army general as a client, and she bluntly attacked Sullivan’s outspokenness as evidence of his bias.

In a June 6 letter to Barr and his deputy, Powell said she was joining Flynn’s defense and called for an independent Justice Department review of his case. Powell cited in part Sullivan’s “tirade” at the hearing, in which the judge rejected a mutual recommendation of probation because of Flynn’s then-substantial cooperation with Mueller’s team.

In Powell’s letter, later disclosed in a court filing, she said the judge “made clear he intends to send him to prison. Judge Sullivan was completely wrong on the facts of the case.”

Others have also griped about the judge’s bluntness. In the Stevens trial, Sullivan once said he was prepared to tell jurors that prosecutors had introduced evidence that they “knew was not true” — an instruction he moderated before giving it to the jury.

“His rulings were all reasonable,” U.S. District Judge Royce C. Lamberth, a longtime colleague and a 1987 Reagan appointee, said afterward. “He does wear his heart on his sleeve sometimes, but so do I. . . . It’s probably not the first quality that comes to mind when you think of a judge.”

In a burglary trial in the mid-1980s early in his career, Sullivan walked off the bench in disgust after a police officer gave conflicting testimony, friend Roscoe C. Howard Jr. has recalled. Sullivan then declared a mistrial because he had prejudiced the case.

“He is passionate, but he understands what he thinks is the right thing, and eventually he does the right thing,” said Howard, a former U.S. attorney for the District of Columbia.

If the government and Flynn do not prevail, before either Sullivan or a higher court, the result could put the onus on Trump to pardon his former aide. In 2018, the president cheered Sullivan’s scrutiny of Flynn’s case at the time, when the judge ordered defense lawyers and prosecutors to turn over FBI records detailing agents’ interview with Flynn in January 2017. Some Flynn allies, including the president, speculated that the judge was probing possible FBI misconduct.

“I think it’s a great thing that the judge is looking into that situation,” Trump told reporters at the time.

By last month, Trump reminded reporters of his power to forgive Flynn’s crime, if not exonerate him of it. “I’m not the judge,” Trump said, “but I have a different type of power.”

Legal experts say Sullivan’s actions in recent weeks open the door for proceedings that could help the judge and public understand why Flynn has now insisted he is innocent after earlier admitting guilt under oath.

Former U.S. prosecutor Randall Eliason said that although it is not clear what Sullivan will ultimately do with Flynn’s case, the judge loathes double talk, whether from police, prosecutors, defense attorneys or the Justice Department.

“Judges,” Eliason said, “don’t like to be manipulated.”

Carol D. Leonnig and Matt Zapotosky contributed to this report.