Gen. Michael Flynn, former national security adviser to US President Donald Trump, leaves Federal Court on December 1, 2017 in Washington, DC.
CNN  — 

Michael Flynn’s court case has become much bigger than whether President Donald Trump’s first national security adviser should go to prison for lying to the FBI. It’s become a referendum on the work of the Justice Department and the decision-making of Attorney General William Barr, a test of the separation of powers and the power of the federal judiciary, and even a crusade for Flynn himself.

Flynn’s case – which he hopes the courts will quickly dismiss after the Justice Department agreed he shouldn’t have been investigated for Russian contacts in 2016 – is in front of three judges on the DC Circuit Court of Appeals on Friday morning. But in recent weeks, the case has shifted from one about Flynn’s admissions of guilt to broader questions of how and when criminal cases can be dropped, even in the most unusual and political of circumstances.

“The Trump presidency is causing us to explore. He’s shining a spotlight on these nooks and crannies the public never thought about that hard,” John Yoo, a former attorney in the Bush-era Justice Department’s Office of Legal Counsel and now a University of California at Berkeley law professor, told CNN when asked about the bigger questions the Flynn case raised.

The Flynn prosecution itself doesn’t raise major constitutional questions, Yoo said.

But the recent turns it’s taken, such as how a judge has hesitated to dismiss it and asked for the opinion of a third-party attorney, do.

Flynn’s guilty plea is still technically in the hands of the trial level judge, Emmet Sullivan of the DC District Court, and Sullivan is considering whether he must dismiss the case or could sentence Flynn. But Flynn challenged Sullivan at the appeals court above him, and that court, the DC Circuit, has pushed Sullivan to defend his orders.

“What Sullivan is doing is turning it into an institutional constitutional question about the power of a judge,” Yoo said.

From the opposite perspective, Deepak Gupta, an appellate lawyer who represents House Judiciary Democrats in the Flynn case, nearly agreed on the case’s gravitas before the Circuit arguments. The appeals court on Friday is questioning not whether Flynn is guilty, but whether Sullivan must dismiss the case immediately and had the power to appoint an outside lawyer to argue against the DOJ’s dismissal.

“There is a serious separation of powers issue here – the judiciary’s ability to police prosecutorial decisions to dismiss cases,” Gupta said.

Gupta, writing for the Democrats, has urged Sullivan to take the time to review the Justice Department’s actions, citing a mechanism in the law that requires prosecutors to ask the judge for permission to dismiss a case.

The power of the judge “is likely to come up in cases that are political, because that was the whole point of the rule” giving judges the leeway to approve dismissals, he said.

Several times now, the Trump administration has pushed the courts into judicial wormholes like these. There were the fights over House subpoenas of banks and an accounting firm for Trump’s records, and standoffs over administration witnesses testifying to Congress during Trump’s impeachment. Those issues are still unresolved by the court system.

Now, with Flynn, the DC Circuit has fast-tracked the debate about Sullivan’s power two years after Flynn pleaded guilty to lying about his contact with Russia during the Trump transition and also admitted to submitting a false document about his foreign lobbying to the Justice Department.

“This is a President who’s testing the ultimates over and over,” said Jeffrey Bleich, former ambassador to Australia during the Obama administration. Bleich now works with two groups – retired federal judges and former national security professionals – that have backed Sullivan reviewing the DOJ’s actions.

The Flynn case, Bleich said, is yet another test of the fundamental structure of American government. “Now, this is a President who wants what he wants. He wants to test the limits and force (other branches) into positions of backing down,” he said. The message in the Flynn case, he said, is “You can get off if you’re a friend of the President. These are fundamental tests.”

The Justice Department has argued they get ultimate control over prosecution decisions, and others have argued the situation is similar to agreements the Justice Department makes to defer decisions to prosecute. But a former federal judge appointed by the court has reasoned this case is unlike those – and that it’s one where what happens to Flynn should be out of the DOJ’s hands. Flynn should be sentenced, the former judge, John Gleeson, wrote earlier this week.

Gleeson, writing to Sullivan on Wednesday, called the DOJ’s moves to exonerate Flynn a “highly unusual effort,” with “strained maneuvers” to marshal a legal theory to dismiss Flynn’s charge.

Ohio Attorney General Dave Yost, who’s authored briefs on behalf of Republican state attorneys general asking the courts to side with the DOJ’s dismissal request, has contemplated bigger questions about why the case has taken on so much more meaning.

“The fact that Flynn admitted he lied, that he was not forthcoming. The notion that all of this is just going to go away bothers people’s sense of morality. The notion that the judge just has to do this, has to let him walk away, bothers people,” he told CNN.

Yost argues that accountability for Flynn could come in other ways – with it becoming a campaign issue voters consider this year or with Congress looking closer at prosecutorial discretion. That argument echoes what Trump’s Justice Department has said in court on other major separation of powers cases, such as in their opposition to the court system enforcing the House of Representatives’ subpoena power.

Because the Flynn case has moved into the appeals court, the legal possibilities have gotten even more complex.

“This is like a set of seven of those Russian nesting dolls. Each one that comes out is different,” Yost said.

“What’s gotten quite interesting now is it makes it really difficult to predict exactly how it’s going to go,” said Ryan Fayhee, a former national security prosecutor who now works at the law firm Hughes Hubbard & Reed. “It’s not exactly a chess match. It’s a little bit like 3- or 4-D chess.”

If the Circuit sides with Flynn in his appeal, it’d be an unusual step, given that the type of appeal Flynn sought, correcting a trial judge’s error, is rarely allowed in court.

If the Circuit dismisses the case immediately, that raises even more possibilities, putting Sullivan in a position where he may want to continue to fight for his power and ask more questions of the Justice Department, which he hasn’t yet formally questioned about its reasons for the dismissal. The three judges who will hear Flynn’s case on Friday include two Republican-presidential appointees who have sided with the Trump administration before. The full DC Circuit, made up mostly of Democratic-presidential appointees, could disagree with what they decide, keeping the case alive for even more court arguments.

And if the appeals court doesn’t move quickly or it sides with Sullivan after Friday, the action returns to Sullivan’s courtroom, where arguments between supporters of the judiciary, the Justice Department and Flynn will continue through the summer.

As for Flynn, he’s also tapped into bigger ideas as the Circuit Court arguments approached. His lawyers have cheered on the DOJ’s dismissal and attacked Sullivan, while his supporters, including family members, have dubbed Friday “#THERECKONING” on Twitter.

On Thursday, the conservative site Western Journal published an op-ed Flynn wrote meditating on God and cultural revolution. “God is the ultimate judge and decision maker. His anointed providence is our country, the United States of America,” he wrote. “As long as we accept God in the lifeblood of our nation, we will be OK. If we don’t, we will face a hellish existence. I vote we accept God.”