Identified in court papers as "John Doe," the man has been held for nearly five months, the military allowing him access to legal advice only after being forced to do so by a federal judge in Washington DC.
He was born in the United States but also has Saudi nationality, and the government has maintained the right to transfer him to another country, presumably Saudi Arabia.
It would be one way -- highly illegal according to rights lawyers -- to handle a fundamental dilemma for President Donald Trump, a test case challenging his pledge to be tough on any captured Islamic State supporters and his commitment to US law.
Between 100 to 200 US nationals traveled to Syria and Iraq after 2010 to work and fight in their ranks, according to various estimates.
A handful are known killed, but the number isn't clear: the US has not provided any data.
'Enemy fighter'
John Doe is the only one known captured alive. On September 14 the Pentagon confirmed that they were holding a US citizen who had been fighting for the Islamic State group and surrendered to the allied Syrian Democratic Forces in Syria days earlier.
He was moved to Iraq where he has been interrogated by military and FBI investigators.
US forces allowed the International Committee of theRed Cross to meet him, but since then have fought to prevent him from gaining legal representation and a hearing in US courts.
The American Civil Liberties Union filed suit to get access to the prisoner. The government refused to provide any information about him -- his name, age, or origins.
They termed him an enemy fighter and claimed he showed no desire for legal representation.
Hearings on his status between September and January were surreal: government lawyers argued he had never expressed the desire for legal representation, though they would not say if he had been asked; that the ACLU had no standing to represent him because they had not been requested; and that the ACLU could not represent the man because they did not know his identity.
In January the judge, Tanya Chutkan, rejected government arguments and ordered them to grant the ACLU access.
ACLU attorney Jonathan Hafetz said that since then they have had several video conferences, and are waiting for a full ruling on a habeas petition.
But meanwhile the government maintains it has an option to transfer him to another country, though never explaining why.
Fundamental rights
"He deserves the basic right of American citizens not to be rendered by their government to a foreign country in the dead of night without judicial review of the basis for their transfer," Hafetz told AFP in an interview.
"They cannot lawlessly transfer an American citizen to another government potentially as a way of defeating the habeas petition."
Hafetz said they now know his identity, but do not want to reveal it, since he has not been formally charged and the government has yet to provide any evidence that he had enlisted in the Islamic State cause.
"The label of enemy combatant is a terrible label, a stigmatizing label, and the government hasn't made any case that he's an enemy combatant."
It's not clear why the government refuses to hand him over to the US justice system, as other Americans accused of terror have been.
But analysts think the Trump administration wants to avoid the fundamental question of whether an American caught fighting for Islamic State has any rights.
They speculate Trump might want to send him to the Guantanamo prison for foreign "war on terror" detainees. On Tuesday Trump reversed an order by his predecessor Barack Obama to shut down Guantanamo, which still has 41 inmates.
Asked what their stance is, the Justice Department declined to answer.
"Our view is that if they want to detain an American citizen, there's only one option: they can charge him with a crime or they can release him," Hafetz said.
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