The Justice Department's surprise motion Thursday to dismiss the case against former national security adviser Michael Flynn has left some legal experts puzzling over how the federal judge presiding over the years-long, politically fraught legal battle might respond.

District Judge Emmet Sullivan has previously excoriated Flynn in court for his actions, including in a December 2018 sentencing proceeding prior to Flynn's later withdrawal of his guilty plea for lying to the FBI.

"You lied to the FBI about three different topics, and you made those false statements while you were serving as the National Security Adviser -- the President of the United States' most senior national security aid. I can't minimize that," Sullivan said. "I mean, arguably, that undermines everything this flag over here stands for. Arguably, you sold your country out."

However, Thursday's filing by the U.S. attorney for the District of Columbia Timothy Shea, handpicked for the position last year by Attorney General William Barr, sought to undercut many of the arguments long accepted by Sullivan in the case as he weighed how to hand down justice.

Though Flynn had previously pleaded guilty twice in court to lying to FBI agents in a January 2017 interview at the White House about his conversations with former Russian Ambassador Sergey Kislyak, Shea said new evidence about the FBI's handling of the investigation at the time rendered its inquiry into Flynn illegitimate.

"The evidence shows his statements were not 'material' to any viable counterintelligence investigation -- or any investigation for that matter -- initiated by the FBI," Shea said. "Indeed, the FBI itself had recognized that it lacked sufficient basis to sustain its initial counterintelligence investigation by seeking to close that very investigation without even an interview of Mr. Flynn."

The language in the filing drew widespread condemnation from many former law enforcement officials, who cast the episode as the latest example of Barr interfering in a criminal case at the benefit of one of President Donald Trump's political allies.

Former President Barack Obama, who previously had warned Trump not to hire Flynn, brought up his concerns about the dismissal of charges in a call with past members of his administration on Friday.

"That's the kind of stuff where you begin to get worried that basic -- not just institutional norms -- but our basic understanding of rule of law is at risk," Obama said, according to leaked audio obtained by Yahoo News. "And when you start moving in those directions, it can accelerate pretty quickly as we've seen in other places."

In an interview with CBS on Thursday Barr denied he was doing the president's bidding and demurred when asked whether it remains true that Flynn lied to the FBI.

"You know, people sometimes plead to things -- that turn out not to be crimes," he said.

Legal experts reached by ABC News said the sequence of events -- which they described as without clear precedent, raises significant questions for Judge Sullivan as he considers whether to accept the Justice Department's motion filed "with prejudice," meaning future prosecutors would be barred from revisiting the charges.

"He's not going to act rashly, he's gonna take his time," said Rory Little, a former associate deputy attorney general and current law professor at UC Hastings. "This is as sensitive a situation as he's confronted."

Former judges and prosecutors pointed to three separate tracks Sullivan could potentially take, each with variations in how he might carry them out.

He could simply accept the Department of Justice's motion for dismissal by taking a "leave of court," which would make way for the charges to be formally tossed out. If Sullivan has more serious concerns about either the conduct of FBI agents outlined in Shea's filing, or suspects potential political influence in the DOJ's decision to dismiss, he could appoint an independent counsel to open an inquiry into the case. Sullivan could also technically decline to accept the Justice Department's motion altogether and move toward sentencing Flynn -- though legal experts suggested this would be unlikely and would face an immediate appeal.

"A situation in which someone has pled guilty twice, litigation has been going on for two years, the main prosecutor withdraws from the case, there's a certain amount of examination that the judge should do," former district judge Nancy Gertner said Friday.

Gertner and others said a likely next step for Sullivan would be calling a conference of the DOJ and Flynn's defense team to press for more answers on Thursday's motion, especially after the case's former prosecutor who served in special counsel Robert Mueller's office, Brandon Van Grack, withdrew from the case hours before the DOJ's motion. No other career prosecutors from the U.S. attorneys office signed onto Shea's filing.

Little pointed to Sullivan's past actions when overseeing the failed corruption case against former U.S. Sen. Ted Stevens, who was convicted in October 2008 of violating federal ethics laws. Stevens later had his conviction thrown out by Sullivan after it was revealed prosecutors failed to turn over exculpatory evidence.

Outraged over the pattern of conduct, Sullivan appointed a cadre of independent lawyers to review whether any involved in the previous case should face criminal charges.

Little said while he wouldn't speculate Sullivan would take similar action to probe the Justice Department's conduct in the Flynn case, he said he could see Sullivan appointing some kind of amicus, or 'friend of the court,' to come in as an independent counsel to advise him on a path forward.

However, taking such action could raise significant procedural and constitutional concerns, others said.

"That sort of situation here with the government and the defense both agreeing that the case should be dismissed, the only way to get an independent view is to have an outside special prosecutor," said retired district judge Shira Scheindlin in a phone interview Friday. "But I don't know if you can do that, because the prosecution is brought in the name of the United States, representing the people of the United States."

Gertner, who served 17 years as a district judge in Massachusetts, said while the rules dictating what steps Sullivan could take in an inquiry appear "ambiguous," she believes the law shows he has a "duty" to seek further answers to get a better understanding of the Justice Department's motivations.

"The law says a leave of court is required unless dismissal is contrary to manifest public interest," Sullivan said. "The question will be whether an obviously pre-textual motion to dismiss, an obviously inappropriate motion to dismiss that came about as a result of untoward political influence, that it seems to me is the only question he can be asking."