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Washington, D.C. federal District Judge Emmett Sullivan is refusing to dismiss the criminal case against former national security advisor Michael Flynn, and is now arguing that the D.C. Circuit Court of Appeals erred when it ordered him to do so last month in a 2-1 ruling.

Sullivan, through his attorney Beth Wilkinson, filed a petition on Thursday for a so-called "en banc" review by the entire D.C. Circuit Court of Appeals, arguing that the three-judge panel was improperly trying to force the district court "to grant a motion [to dismiss] it had not yet resolved ... in reliance on arguments never presented to the district court."

Flynn's lawyer, Sidney Powell, successfully sought a writ of mandamus last month from the three-judge panel on the appellate court ordering Sullivan to toss the case. Writs of mandamus are unusual remedies that order government officials to take a certain action; they are appropriate when there has been a "usurpation of judicial power" that is "clear and indisputable," Powell acknowledged.

Powell, whose argument was supported by the Justice Department, primarily asserted that the constitutional separation of powers, and D.C. Circuit case law, clearly holds that judges cannot unilaterally keep prosecutions alive when both the prosecutors and the defense seek to dismiss charges. The DOJ moved to dismiss the Flynn case earlier this year after a slew of exculpatory information, which the government acknowledged should have been disclosed long ago under a standing court order, was finally turned over to the defense team.

READ THE JUDGE'S PETITION FOR EN BANC REVIEW

But, the circuit court's panel decision ordering the dismissal of the case, Sullivan argued, was premature, and threatened to turn "mandamus into an ordinary litigation tool."

"All the district court has done is ensure adversarial briefing and an opportunity to ask questions about a pending motion," Sullivan's motion reads. "Outside the panel opinion, those actions have not been considered inappropriate—much less an extreme separation-of-powers violation justifying mandamus."

If en banc review is granted, an oral argument date would then be set, likely in the fall. If en banc review is denied, Sullivan could appeal to the Supreme Court -- a process that could take months to resolve, past Election Day.

The Department of Justice has agreed with Powell's arguments, saying in court filings that Sullivan risked compromising the separation of powers between the executive and judicial branches.

"This Court should issue a writ of mandamus compelling dismissal," the DOJ wrote in a filing signed by Solicitor General Noel Francisco last month, who ordinarily represents the government before the Supreme Court. Francisco's imprimatur was significant, and indicated the DOJ was taking Sullivan's actions seriously.

BOMBSHELL FLYNN DOCS DROP PROMPT NEW REVIEW ..... SULLIVAN HINTS DOJ MAY BE BIASED

"Under Articles II and III of the Constitution, the power to prosecute belongs to the Executive, not the Judiciary," the government continued. "Federal Rule of Criminal Procedure 48, read against the backdrop of that constitutional principle, required the district court to grant the government's motion to dismiss the indictment with prejudice because that motion was unopposed." That rule of procedure states: "The government may, with leave of court, dismiss an indictment, information, or complaint."

In her own filings, Powell heavily cited the 2016 D.C. Circuit court case United States v. Fokker Services for the proposition that a "district court cannot deny the Government’s motion to dismiss because the judge has 'a disagreement with the prosecution’s exercise of charging authority,' such as 'a view that the defendant should stand trial' or 'that more serious charges should be brought.'" The DOJ filed its own brief backing up Powell, and appellate panel largely argreed in its ruling.

But on Thursday, Sullivan essentially said the "Fokker" citation wasn't applicable. He argued, in seeking en banc review, that "[the] Fokker [case] did not question the process the district court employed in reaching [its] erroneous decision." Specifically, Sullivan's filing asserted that the Fokker court expressly declined to apply its reasoning to less "formal judicial action," and that Sullivan was merely considering his options as to how to proceed with the Flynn case -- which, Sullivan said, was allowed under current precedent.

Ryan Fayhee, an attorney at Hughes Hubbard & Reed who previously served as a top prosecutor and national security official at the DOJ, told Fox News the Fokker case was indeed distinguishable from the facts of the Flynn case.

Fokker "concerned a deferred prosecution agreement, and not a knowing and voluntary guilty plea," Fayhee said, in an argument echoed by Sullivan's filing on Thursday. "In that case the judge’s role was ministerial and limited to whether the Speedy Trial Act could be extended in the interest of justice; it did not consider whether the Justice Department may dismiss a case post-plea (an unprecedented and novel issue); nor whether a district court judge may initiate a contempt proceeding as is being considered here."

Sullivan pointed to the 1973 D.C. Circuit case United States v. Ammidown for the precedent that even where the defendant "concurs" in the dismissal of a case, it was appropriate for judge's to "obtain and evaluate" prosecutors' reasoning, to better serve the "public interest." Democrats, and even Sullivan's attorney, have suggested political bias could be behind the DOJ's decision to seek dismissal.

Even if Ammidown was improperly decided, Sullivan said in the brief, mandamus was not the appropriate remedy to resolve the matter.

However, Ammidown's case law concerning motions to dismiss is "dicta," or nonbinding on future courts, because it was not central to the case's final holding. The Ammidown court noted that "Rule 48(a) [governing motions to dismiss] does not apply as such to the case at bar, but study of the judicial role in dismissals illuminates our course."

The ruling by the three-judge panel that agreed with Powell and the DOJ had expressly ordered that Flynn’s petition for a writ of mandamus "be granted in part; the District Court is directed to grant the government’s ... motion to dismiss; and the District Court’s order appointing an amicus is hereby vacated as moot, in accordance with the opinion of the court filed herein this date."

Bill Priestap, assistant director of the FBI's Counterintelligence Division, testifies during a Judiciary Committee hearing into alleged Russian meddling in the 2016 election on Capitol Hill in Washington, U.S., July 26, 2017. REUTERS/Aaron P. Bernstein - RC1733A448D0

Ex- assistant director of the FBI's Counterintelligence Division Bill Preistap, seen here in 2017, authored a memo suggesting the FBI debated getting Michael Flynn "fired." (Reuters)

The DOJ, Powell said, had ample reason to seek the dismissal of Flynn's case, in light of newly released exculpatory information. "Now additional facts have established he was not interviewed for a legitimate purpose, and therefore any statements he made were not 'material' under 18 U.S.C. §1001, the Government justly believes that he is not guilty of any crime," Powell wrote in a filing last month.

For example, handwritten notes that surfaced earlier this year -- written by Bill Priestap after a meeting with then-FBI Director James Comey and then-FBI Deputy Director Andrew McCabe -- suggested that agents planned to interview Flynn at the White House on January 24, 2017 "to get him to lie, so we can prosecute him or get him fired."

In the alternative, Priestap's note suggested that a possible goal was to get Flynn "to admit to breaking the Logan Act" when he spoke to Russia's then-Ambassador Sergey Kislyak during the presidential transition period.

The Logan Act has never been successfully used in a criminal prosecution and has a questionable constitutional status; it was enacted in 1799 in an era before telephones, and was intended to prevent individuals from falsely claiming to represent the United States government abroad.

Priestap's memo surfaced this summer even though the Justice Department and FBI had been under an obligation to turn over all relevant, potentially exculpatory materials to Flynn's legal team since February 2018.

Attorney General Bill Barr had appointed U.S. Attorney Jeff Jensen to review the DOJ's handling of the Flynn case, and Jensen apparently unearthed the documents.

FOX News' Bill Mears and David Spunt contributed to this report.