WASHINGTON — After commandos and F.B.I. agents snatched a key suspect in the 2012 attack on an American diplomatic compound in Libya, some Republican lawmakers urged the Obama administration to take him to Guantánamo Bay, Cuba, for a military trial, sounding what has become a common refrain — that a civilian trial for a terrorist is, among other things, too dangerous.
But on Monday, the defendant, Ahmed Abu Khattala, was ushered into a federal courthouse here, pleading not guilty to new charges that make him eligible for the death penalty. And for all the talk of security concerns, he appeared — as he had before — in open court, not behind the bulletproof glass reserved for particularly dangerous defendants. The hearing itself was routine, which is what made it so remarkable.
Five years ago, the debate over whether terrorists should be prosecuted in criminal courts was so contentious that it made its chief advocate, Attorney General Eric H. Holder Jr., a political liability. Republicans argued that F.B.I. interrogation was not suited to wartime intelligence-gathering. By extension, civilian courtrooms were no place for terrorists, who did not deserve the same rights as common criminals.
But as Mr. Holder prepares to leave office, his success in reversing the Bush administration’s emphasis on trying terrorism suspects in secret prisons or at offshore military tribunals may be one of his most significant achievements. While he did not end the debate — each new arrest brings fresh statements of disapproval from critics — the Justice Department can now point to a string of courtroom victories that his liberal supporters, as well as many law enforcement officials, believe has reshaped the government’s approach to prosecuting terrorism.
“History will remember these years as the time when we resolved one of the most contentious debates in the post-9/11 era: about whether our legal system was equipped to handle national security cases,” Mr. Holder said recently in a written response to questions about the issue.
In recent years, the Justice Department has won a guilty plea from a Somali national who admitted supporting the terrorist group the Shabab; sent Osama bin Laden’s spokesman, Sulaiman Abu Ghaith, to prison for life; begun criminal proceedings against a Libyan suspect from Al Qaeda; and, most recently, set a death penalty case in motion against Mr. Khattala.
While the political controversy has largely subsided, particularly on the issue of whether the trials themselves pose a risk, critics such as Senator Lindsey Graham, Republican of South Carolina, say the administration has simply delayed an important debate on what they view as the preferable alternative of holding terrorism suspects outside the normal justice system.
“If there is another terrorist attack, that’s when this becomes very important,” Mr. Graham said. “When we look back and say, ‘Did we miss the opportunity to gather intelligence by criminalizing the war?’”
After the Sept. 11 terrorist attacks, many in the government did fault the Clinton administration for treating terrorism as a criminal matter and not recognizing that Al Qaeda had declared war on the United States. So, under President George W. Bush, terrorism suspects were interrogated in secret locations or at the Guantánamo Bay military prison.
Mr. Holder, a former prosecutor and judge, came to office promising to use America’s judicial system, with all its rights and due process, in the fight against terrorism. But on Dec. 25, 2009, a Nigerian operative of Al Qaeda, Umar Farouk Abdulmutallab, tried to blow up an airliner over Detroit using a bomb hidden in his underwear.
After questioning him for 50 minutes, F.B.I. agents read Mr. Abdulmutallab the Miranda warning. He stopped cooperating for several weeks, prompting a political furor over whether the Justice Department’s focus on collecting evidence for trial made it incapable of gathering intelligence in the war against Al Qaeda.
The next month, with the controversy over Mr. Abdulmutallab lingering, the White House reversed a decision to prosecute Khalid Shaikh Mohammed, the admitted mastermind of the Sept. 11 attacks, in a Manhattan courthouse. Republicans had criticized Mr. Holder, saying that he saw foreign terrorists as common criminals with the same rights as Americans. New York politicians from both parties had said a civilian trial would make the city a terrorist target.
At the Justice Department, officials saw it as a matter of principle. The legal system embodied America’s values, they said, and the country did not need to change those values to defeat Al Qaeda. But on Capitol Hill, the controversy over the Sept. 11 trial became part of a larger debate over the future of Guantánamo Bay and interrogation.
As Senator Kelly Ayote, Republican of New Hampshire, put it, “The issue has never been whether our civilian court system can obtain convictions, but how we can best collect the intelligence necessary to protect our country.”
Many F.B.I. agents had opposed the Guantánamo Bay tribunals for years. Some had a principled objection, that America should not rewrite its system of justice. Others saw it practically: It made no sense to write the Justice Department and criminal courts, with their long track record, out of the process in favor of tribunals at Guantánamo Bay, which had produced spotty results.
“I thought the whole thing was stupid and politically motivated, and it made us less safe,” said James McJunkin, the former head of counterterrorism at the F.B.I. The Justice Department held out hope. A former Guantánamo Bay detainee, Ahmed Khalfan Ghailani, was already set to stand trial in New York for his role in terrorist attacks in 1998. A conviction, prosecutors hoped, would assure critics that terrorism suspects could be prosecuted safely and receive lengthy sentences. Instead, a jury acquitted Mr. Ghailani on all but one of 280 charges.
It did not matter that he received a life sentence for that charge, or that the tribunals at Guantánamo Bay had proved far less likely to produce such a harsh sentence. The case renewed criticism that the Justice Department was not equipped to fight terrorism.
But in April 2011, prosecutors caught a break when the military captured a Somali terrorism suspect aboard a fishing boat in the Gulf of Aden, between Yemen and Somalia. Officials held the man, Ahmed Abdulkadir Warsame, for months aboard a Navy ship, where he was questioned first by intelligence officials, then by F.B.I. agents who advised him of his rights. When the interrogation was complete, Mr. Warsame was delivered to New York and arraigned in a civilian courtroom.
Some lawmakers criticized the decision, saying Mr. Warsame should have been taken to Guantánamo Bay. But with the court case underway, the administration weathered the criticism largely by ignoring it. “The way to sell it politically was to just do it,” said Matthew Miller, Mr. Holder’s former spokesman.
The administration has not faced a high-profile test of the policy, such as the capture of Al Qaeda’s leader, Ayman al-Zawahri. But officials believe that this model — capture, interrogate and prosecute — can be replicated in the war against the jihadist group the Islamic State. Meanwhile, the Guantánamo Bay tribunals have faltered. Two people have gone to trial and been found guilty there. Both had their convictions overturned by an appeals court, though one has since been reinstated.
“We have shown, time and again, that upholding the rule of law is not inconsistent with safeguarding our national security,” Mr. Holder said recently. “We have honed an approach to apprehending, questioning and convicting terrorism suspects that I think will serve as a blueprint for years to come.”