Michael Flynn FILE
CNN  — 

The Justice Department’s decision to drop the criminal case against former Trump national security adviser Michael Flynn was a “corrupt and politically motivated favor,” a former judge who was appointed to analyze the case said Friday in a new court filing.

John Gleeson’s comments Friday include some of the sharpest rebukes of the Justice Department to date and directly accuse President Donald Trump’s appointees of doing his bidding to protect Flynn merely because he is a political ally.

“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 wrote.

“Yet that is exactly what has unfolded here,” he added.

He reiterated his position that Judge Emmet Sullivan should reject the Justice Department’s request to dismiss the case, and should move forward with Flynn’s sentencing.

As part of the special counsel investigation, Flynn pleaded guilty in 2017 and admitted that he lied to the FBI about his Russian contacts. But the Justice Department announced in May that it was abandoning the case, and asked to formally drop the charge. In response, Sullivan appointed Gleeson and directed him to rebut the Justice Department’s position.

In short order, Gleeson urged Sullivan to keep the case alive and sentence Flynn for lying to the FBI and for committing perjury during the court proceedings, when he walked back his previous guilty plea. Flynn asked for an emergency order from the DC Circuit Court of Appeals, and won a temporary victory that would’ve ended the case – but that ruling was then reversed last month.

“The Government is trying to give special treatment to a criminal defendant because he is favored by the President,” Gleeson wrote, arguing that the judge “would send an important message about the rule of law by refusing to accord special treatment to (Flynn’s) perjury.”

It’s up to Sullivan to decide how to proceed, though if he decides to keep the case alive, Flynn could appeal that decision, leading to more legal limbo.

Blistering rebuke

In the court filing, Gleeson mounted a stinging and flourish-filled rebuke of the Justice Department, and even claimed its actions in the case were “unworthy of our justice system.”

“To describe the Government’s Motion to Dismiss as irregular would be a study in understatement,” Gleeson wrote.

Gleeson accuses the Justice Department of invoking a “parade of false formalities” and using “straw man” arguments to protect Flynn.

Pushing back against the Justice Department’s assertions that Flynn’s lies weren’t material to the Russia investigation, Gleeson cited the recent bipartisan report from the Senate Intelligence Committee. The committee said it investigated Flynn and other Trump aides’ contacts with Russians “in order to more fully understand what Moscow sought to gain” from Team Trump.

In asking to drop the case, prosecutors said they weren’t sure they could prove that Flynn’s statements to the FBI were actually false. Gleeson wrote that “Flynn has repeatedly confessed,” and said that his “numerous and consistent confessions should all but settle the question.”

Legal limbo

Flynn was a key witness in special counsel Robert Mueller’s investigation into Russian meddling in the 2016 election and potential obstruction.

But Flynn switched up his legal team last year and took a new approach: He started claiming that there was misconduct by Mueller’s prosecutors and started leaning on conspiracy theories in his court arguments. Earlier this year, he asked to withdraw his guilty plea two weeks before he was set to be sentenced, and his attorneys proclaimed his innocence in court documents.

Months later, the Justice Department announced its intention to drop the case, an extraordinary reversal after spending years prosecuting Flynn. The decision came while Trump lashed out against the Mueller investigation and while Attorney General William Barr took steps to unwind some of Mueller’s achievements.

The case has been stuck in legal limbo ever since, though Gleeson’s filing on Friday was one of the last procedural steps on the schedule before Sullivan can move forward.

For his part, Flynn and his lawyers say he is innocent and that he was only ensnarled in the Russia investigation because of abuses by Mueller and senior Obama administration officials. His plight has become a rallying cry for Trump and right-wing media outlets, which have promoted many of his theories, even though there is almost no evidence to back it all up.

While his case snaked through the court system this summer, Flynn and some of his conservative lawyers started embracing the QAnon conspiracy theory movement, and Trump even said he’d consider bringing Flynn back into the administration if he wins a second term.

CNN’s Katelyn Polantz contributed to this report.