WASHINGTON — Two decades ago, the Bush administration said its “war on terror” prisoners held at Guantanamo Bay were off-limits to the federal courts, but the Supreme Court disagreed.

“A state of war is not a blank check for the President,” said Justice Sandra Day O’Connor in 2004. “Whatever power the U.S. Constitution envisions for the Executive in its exchanges with other nations or with enemy organizations ... it most assuredly envisions a role for all three branches when individual liberties are at stake.”

Only Justice Clarence Thomas dissented.

That issue is now back before the Supreme Court.

Although the nation is not at war, President Donald Trump has invoked his war powers under the Alien Enemies Act of 1798 to round up and deport to El Salvador about 200 alleged members of a Venezuelan crime gang.

Two legal questions arose immediately.

How can Trump rely on the 1798 law, which applies only when Congress has “declared war” or a “foreign government” has launched an “invasion”?

And how does the government know all these men are gang members? Their families said they have no criminal records, and in some instances, fled Venezuela and sought asylum to escape the gangs.

So far, however, the legal fight has focused on the same big question from the Guantanamo era: Do federal judges have the authority to limit the power of the president who says he is protecting the nation from “dangerous aliens”?

On Friday, Trump’s acting Solicitor General Sarah Harris urged the Supreme Court to set aside the judge’s order that put a temporary pause on further deportations.

“This case presents fundamental questions about who decides how to conduct sensitive national-security-related operations in this country — the President ... or the Judiciary,” she wrote in her appeal. “The Constitution supplies a clear answer: the President. The republic cannot afford a different choice.”

The justices asked for a response from the American Civil Liberties Union by Tuesday. The fast-moving case poses an early test of whether the high court will uphold the president’s power to swiftly deport migrants without interference from judges.

Two weeks ago, Trump signed a proclamation that Tren De Aragua, a Venezuelan crime gang, was “perpetrating ... an invasion” of the United States and ordering the “prompt removal” of all those who were held.

On the afternoon of Saturday, March 15, U.S. District Judge James Boasberg convened a hastily arranged hearing in response to an emergency lawsuit brought on behalf of five Venezuelan men who feared they would be deported to El Salvador.

At the same hour, administration officials were arranging for three planes to take off from Texas.

The judge questioned how the 1798 law could authorize such deportations, and “to preserve the status quo,” he ordered a temporary pause on all the deportations.

Although the five named plaintiffs stayed in Texas, the administration essentially ignored the broader order and allowed the three flights to proceed as planned.

Although the judge said he was troubled his orders were ignored, Trump’s lawyers were troubled by his intervention.

“These orders are an affront to the President’s broad constitutional and statutory authority to protect the United States from dangerous aliens who pose grave threats to the American people,” they said on behalf of Attorney General Pam Bondi.

“The presidential actions they challenge are not subject to judicial review,” they said.

“The Constitution simply provides no basis for ... second-guessing the policy judgment by the Executive that such an ‘invasion’ is occurring,” they said. The president “has an inherent authority to conduct foreign affairs and address national security risks.”

They took a hard line and refused to even disclose the flight times for airplanes that flew to El Salvador.

That’s a “state secret,” they said in a brief filed Monday.

Veterans of the legal battles over Guantanamo see some similarities but differences as well.

University of California, Berkeley law professor John Yoo, a former Bush administration attorney, said the Guantanamo prisoners were not brought into the United States.

“Here, there is no doubt that the Venezuelans sent to El Salvador were detained within the United States,” he said.

In the past, the Supreme Court has said people who are being held in this country, including noncitizens, have a right to due process of law.

Yoo said, “Trump is invoking the same arguments we made after 9/11 that the capture and detention of enemy prisoners during wartime fell exclusively within the president’s authority as commander-in-chief to conduct war.” He is also “making similar arguments as to why federal judges today should defer to the decisions of the executive branch during what he has determined is an invasion.”

But Yoo said he doubts the courts will uphold Trump’s reliance on the 1798 law.

Earlier this week, Boasberg explained his order was narrow in scope as well as temporary. It would not lead to the release any of the Venezuelans that are being held, and it does not prevent the government from deporting those who have a “final order of removal” under the U.S. immigration laws, he said. It prevents only deportations to El Salvador that are based on the disputed Alien Enemies Act.

It also resolved nothing about the plight of those who are now held in El Salvador.

On Monday, Trump’s lawyers asked the D.C. Circuit Court of Appeals to throw out Boasberg’s order but lost in a 2-1 decision.

Each of the judges wrote a lengthy opinion making a separate point.

Judge Karen Henderson, an appointee of President George H.W. Bush, disputed the use of the Alien Enemies Act. “An invasion is a military act, not one of migration,” she said.

Judge Patricia Millett, an appointee of President Barack Obama, said the detained men deserve a hearing to challenge the claim they were gang members.

Judge Justin Walker, a Trump appointee, dissented but said the detained men could file a habeas corpus claim in Texas where they are held.

ACLU attorney Lee Gelernt, who brought the lawsuit, said the decision preserving the judge’s order “means that hundreds of individuals remain protected from being sent to a notorious black-hole prison in a foreign country, without any due process whatsoever — perhaps for the rest of their lives.”

Skye Perryman, president of Democracy Forward, called the D.C. Circuit’s decision “an important step for due process and the protection of the American people. President Trump is bound by the laws of this nation, and those laws do not permit him to use wartime powers when the United States is not at war and has not been invaded.”

In her appeal on Friday, Harris, the acting solicitor general, agreed with Walker that the Venezuelans held in Texas could file a writ of habeas corpus there.

ACLU attorneys and Millett dismissed that option as impractical. The hundreds of men who were held had no lawyers, they said, and no way to know they must file an individual legal claim in federal court.

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