The Trump administration is weighing how to proceed with a U.S. citizen it has held as an enemy combatant since September in a unusual case that could threaten the legal underpinnings of the war against the Islamic State in Iraq and Syria (ISIS).

The man, known only as John Doe, has presented a difficult case for the administration since he was first picked up by Syrian Democratic Forces as an alleged ISIS fighter and turned over to the U.S. eight months ago.

Officials believe they lack sufficient useable evidence to try him in court, but for security reasons, are loathe to simply release him.

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A D.C. appeals court on Monday blocked the government from transferring Doe to Saudi Arabia, where he also holds citizenship, further limiting the administration’s options and raising the possibility that the Trump administration could take the case to the Supreme Court.

The administration is also bracing for a possible ruling by a separate federal judge that the government lacks the authority to detain Doe in the first place. It’s unclear when this decision will come down, but it could mark the first time the courts have weighed in on the controversial legal rationale that both the Trump and Obama administrations have used to justify the use of force against ISIS.

The Justice Department said this week that it is “reviewing [the appeals court] decision and considering our next steps.”

“Both domestic and international law confer on the U.S. military broad discretion over battlefield operations, including the transfer of individuals captured on overseas battlefields,” it said.

In the meantime, Doe remains in U.S. military custody in Iraq, where he is being represented by the American Civil Liberties Union (ACLU).

According to the government, Doe attended ISIS training in Syria starting in March 2015. There, he swore allegiance to a deputy of ISIS’s leader, Abu Bakr al-Baghdadi, a man named Abu Hafs al-Maghrebi.

He was assigned to be a fighter in the Zarqawi Brigade, a military unit that “guard[ed] the front lines” in Syria, where he procured fuel for ISIS vehicles, handled expenses and “performed other administrative tasks.” Later, he was tasked with guarding the gate of an ISIS oil field and monitoring personnel who worked on ISIS’s heavy equipment.

There is no public evidence that he took up arms on behalf of ISIS.

Ultimately, Justice Department lawyers say, Doe worked for ISIS for about two and a half years — “until air strikes and other military offensives against [ISIS] forced him to flee.” Syrian forces picked him up at a checkpoint as he was trying to escape Syria into Turkey. He identified himself as an American and said he wanted to turn himself in.

He was dressed in a style “typical of an [ISIS devotee],” the government claims, and "identified himself as 'daesh' — another word for ISIS."

And he was found carrying thumb drives containing ISIS personnel spreadsheet and “military style handbooks” about bomb building, interrogation techniques and weapons handling.

Doe maintains that he went to Syria to document the violence here, not to join ISIS.

But the details of his story have left some legal analysts surprised that the government doesn’t believe it has sufficient evidence to bring a basic terrorism charges against him — the most obvious solution that both the Obama and Trump administrations have leveraged with U.S. persons suspected of aiding ISIS.

“Looks to me, in short, like the government does indeed have the option of pursuing what almost certainly would turn out to be a 20-year sentence,” writes Bobby Chesney, a national security law professor who worked on detention issues at the Justice Department in 2009.

The apparent disconnect has lead to some speculation that the government may be looking for a way to keep Doe out of the country permanently, perhaps by convincing him to renounce his U.S. citizenship. Yasar Hamdi, another U.S.-Saudi citizen who contested his status as an enemy combatant in court in the early 2000s, agreed to a voluntary transfer to Saudi Arabia in exchange for abandoning his U.S. citizenship.

When it first became public that the government was weighing transferring Doe to Saudi Arabia, in December, the ACLU accused the Trump administration of trying to pressure Doe to renounce his citizenship.

The government denied those accusations at the time, asserting that “the USG has not authorized any representative to discuss with the detainee the possibility that he might renounce his U.S. citizenship. Nor does the USG have any information that anyone has attempted to coerce him into doing so."

Jonathan Hafetz, the ACLU lead attorney representing Doe, told The Hill in an email Friday that “to our knowledge” no such conversations have taken place since December, either.

There is another option for the government. It could simply release Doe in Iraq, where he is being held presumably somewhere in the Kurdish region. He could walk free — or he could be immediately snatched up by Iraqi security forces and transferred to Saudi Arabian custody anyway, a move that could suggest the appearance of behind-the-scenes coordination with the U.S.

The Department of Justice, this week, maintained that Doe’s alleged activities with ISIS “implicate numerous national security, law enforcement, international relations and foreign policy concerns.”

If it is not going to charge or release Doe — and lacking the current authority to transfer him — the government is now at the mercy of the judicial system.

There are two distinct court cases surrounding the government’s handling of Doe — but both now turn on the issue of whether it is legally able to hold him as an enemy combatant in the first place.

Critically, Doe is arguing that because ISIS is not explicitly covered under the current congressional authorization for the use of military force — a subject of intense debate across multiple administrations — he cannot legally be held as an enemy combatant.

The federal courts have not weighed in on that issue and a ruling against the government’s longstanding interpretation that ISIS is an “associated force” of al Qaeda could upend the entire legal basis for military action against the terror group.

In a two-to-one split, the appeals court weighing whether the government could legally transfer Doe concluded that that authority rested on the precondition that he is being legally held in the first place — in other words, the government only has the power to transfer Doe if the courts agree that he is a lawfully held enemy combatant.

“Neither the legal inquiry nor the factual inquiry has taken place in this case,” Judge Sri Srinivasan writes.

That very question — whether Doe is being legally held — has been languishing before U.S. District Court Judge Tanya Chutkan now for months.

In the meantime, the government must decide amongst a limited set of unpalatable options: Continue to hold Doe indefinitely while waiting for Chutkan to hand down a potentially adverse ruling — or race the clock and try to win an appeal allowing it to transfer him.

There is no sign of when she will rule.