Attorneys for former national security adviser Michael Flynn and the Justice Department returned to court Tuesday in their push to convince a federal judge to throw out his criminal case after he admitted to lying to the FBI in 2017 about his contacts with the Russian ambassador.

The Justice Department's surprise reversal and motion to drop the case this past May was not immediately accepted by D.C. District Judge Emmet Sullivan, who instead moved to appoint an outside former federal judge tasked with arguing against the DOJ -- as well as considering whether Flynn committed perjury in contradicting his previous guilty plea.

Former judge John Gleeson, the court-appointed 'amicus,' excoriated the Justice Department in a recent filing, arguing its move to drop the charges against Flynn was part of an openly political effort to benefit an ally of President Donald Trump.

“In the United States, Presidents do not orchestrate pressure campaigns to get the Justice Department to drop charges against defendants who have pleaded guilty — twice, before two different judges — and whose guilt is obvious,” Gleeson said. "There is clear evidence that this motion reflects a corrupt and politically motivated favor unworthy of our justice system."

At Tuesday's hearing, acting principal assistant U.S. attorney Kenneth Kohl took issue with Gleeson's accusations, saying materials uncovered by the DOJ in its review of the FBI's investigation fully justified its decision to seek to drop the case.

"The allegations against our office that we would somehow operate, or act with a corrupt political motive just are not true," Kohl said. "I've never seen it in my entire career in our office, and it didn't happen here."

Attorney General William Barr has said he approved the decision to drop the case based on a recommendation from U.S. Attorney Jeffrey Jensen, who he had appointed to review the FBI's actions before interviewing Flynn. Barr said the review led him to determine that the probe of Flynn was not in itself legitimate so his lies were not "material" to any investigation.

Barr has denied his intervention in the case -- just one in a series of controversial moves aligned with Trump's political interests -- was in any way motivated by politics.

Tuesday's hearing followed months of speculation as to how Sullivan might respond to the DOJ's actions after Flynn's attorneys recently lost their appeal to have a higher court overrule Sullivan and order him to dismiss the case.

In one exchange, Sullivan raised a letter that Flynn's attorney Sidney Powell personally sent to Attorney General Barr in June of 2019 in which she requested he investigate the conduct of FBI officials who investigated Flynn. Sullivan described the letter as "highly unusual" and requested the DOJ provide him with any response Barr may have sent her -- though Powell later told Sullivan that Barr never personally responded to her.

Sullivan then pressed Powell directly over whether she has communicated with Trump about Flynn's case -- and appeared to grow irritated as Powell argued she shouldn't have to answer based on potential privilege issues.

Powell later conceded that she did speak with Trump and a legal adviser to Trump about the case "within the last couple of weeks" to provide an update on the status of the case and ask that Trump not pardon Flynn.

Powell went on to argue that Sullivan's actions in the case and his questioning during the hearing proved he was biased and unfit to issue any future rulings on the case and said she would be submitting a motion imminently demanding that he recuse himself.

In questions to the Justice Department, Sullivan inquired about the options he has in considering the government's motion to dismiss -- and what the government might do if he were to accept it but "without prejudice," which would leave open the possibility that a future DOJ could bring charges against Flynn for his lies to the FBI.

Deputy Assistant Attorney General Hashim Mooppan answered that the DOJ was requesting he dismiss "with prejudice," which would prevent such an effort. He separately acknowledged that it's possible Flynn could face prosecution in the future for uncharged criminal conduct he admitted in his initial guilty pleas.

Mooppan later told Sullivan that Barr had personally authorized him to tell the court that his "decisions in these cases are not based on communication to the president, or the White House, and they weren't based on any of the tweets" Trump has sent attacking Flynn's prosecution.

He also echoed statements from Attorney General Barr in a past interview with ABC News, in which Barr said Trump's tweets regarding criminal matters before the department were making it "impossible" to do his job.

"The Attorney General himself said that all of the tweets make his job harder. It makes our job harder too because it's easy to look at the tweets and draw correlations that just aren't really true," Mooppan said.

Gleeson, by contrast, argued that Sullivan should absolutely consider the tweets in his determination of whether to dismiss the case because, he argued, it shows the DOJ's "real reasons" behind its unusual actions.

"The only inference you can draw is that the Justice Department has done exactly what the Attorney General has said is the danger of these tweets -- which is yielding to the president's pressure," Gleeson said.

Sullivan also raised issue with a letter submitted to the court Monday by former FBI attorney Peter Strzok who said that personal notes of his that the Justice Department provided to support its contention that Flynn's prosecution was improper appeared to have been "altered."

"Quite frankly, I was floored when I saw the letter from the attorney that there were mis-alterations in an email," Sullivan said, adding the development was "unsettling" and that he would be asking the government to certify whether all documents that have been provided to the court are authentic.