Such schemes have already stirred considerable controversy elsewhere in the world, including in Great Britain, where since 2005 some three dozen terror suspects have been detained for a time under house-arrest-like conditions, in some cases being required to wear ankle monitors, obey curfews, and refrain from using phones or the Internet. In America, such a compromise is sure to alarm many human-rights advocates and civil libertarians, who regard indefinite detention as antithetical to the American legal system’s most basic tenets. Alberto Mora, a Republican lawyer who, as general counsel of the Navy, broke with the Bush Administration after concluding that some of its brutal counterterrorism policies were potential war crimes, warns, “We simply can’t have indefinite detention. Due process and fundamental fairness make that clear.”

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Marri himself is cautiously hopeful. Despite restrictions on his consumption of television and print news, he followed the Presidential campaign from inside the brig. According to Hafetz, “He’s happy about Obama, but worried he won’t be able to fulfill all the promises and expectations.” Through his lawyers, Marri, speaking publicly for the first time, said, “I am not asking to be taken at my word and to be released, although I very much want to go home to my family. All I am asking for is to be treated like every other person in the United States who is accused of a crime, including terrorism, and to be given a fair trial in an American court.”

As a candidate, Obama promised a sharp break with the Bush Administration’s counter terrorism policies. In a written statement for the Boston Globe, Obama, who taught constitutional law in the nineteen-nineties, said, “I reject the Bush Administration’s claim that the President has plenary authority under the Constitution to detain U.S. citizens without charges as unlawful enemy combatants.” (In fact, the Bush Administration went beyond this claim, arguing that Congress had explicitly granted the President this authority, in a bill passed after the attacks.) In the Globe, Obama went on, “The detention of American citizens, without access to counsel, fair procedure, or pursuant to judicial authorization, as enemy combatants is unconstitutional.” In his Inaugural Address, Obama further underscored his differences with Bush in this area, saying, “As for our common defense, we reject as false the choice between our safety and our ideals.” A top legal adviser to Obama told me that the President also believes that legal residents in America, like Marri, are entitled to due process.

Former Bush Administration officials who were involved in its anti-terror program suggest that Obama may find it harder than expected to translate idealistic rhetoric into action. “Governing is different from campaigning,” says Bellinger, who predicts that Obama and his officials will soon discover that “they can’t just set the clocks back eight years, and try every terror suspect captured abroad in the federal courts.” Bellinger now says that the treatment of Marri was a “failed experiment.” John Ashcroft, who was Attorney General when Marri was designated an enemy combatant, makes no such apologies. Interviewed just before the Inauguration, he defended what he described as a “sound decision” to “maximize the national interest,” and predicted that, in the end, President Obama’s approach to handling terror suspects would closely mirror his own: “How will he be different? The main difference is going to be that he spells his name ‘O-b-a-m-a,’ not ‘B-u-s-h.’ ”

So far, the Obama Administration has declined to state a position on the Marri case. It’s already becoming apparent, though, that Ashcroft was mistaken in his broader point. Obama, in his first week in office, issued three executive orders, undoing many of the most controversial elements of the Bush Administration’s detention and interrogation programs. Most notably, Obama declared that the Administration hoped to close Guantánamo within a year. A little noticed memorandum issued at the time of the orders was dedicated to Marri. It called for a Cabinet-level inter-agency task force, led by Attorney General Eric Holder, to review Marri’s case, with an eye toward finding alternative ways to deal with him.

The same officials will review the status of the enemy combatants held in Guantánamo. The Obama Administration has indicated that it hopes to return the majority of the detainees to other countries, or to try them in civilian and military courts. The looming question, however, is whether there is a category of terror suspect whose status precludes such options. It’s unclear whether some home countries can provide fair trials or secure prisons. More important, the high standard of evidence required in U.S. courts—guilt must be proved “beyond a reasonable doubt”—might result in dangerous individuals being set free.

Qatar has made known its interest in having Marri come home. But the Obama Administration has to decide whether he poses a recidivism risk—an assessment that has to be made, in part, on the basis of statements elicited through torture. (Khalid Sheikh Mohammed, the self-described mastermind of the 9/11 plot, was waterboarded by the C.I.A., and reportedly said that Marri was a fellow-terrorist.) As such, Marri may exemplify what Greg Craig, Obama’s White House counsel, calls “the toughest question” facing the Administration as it tries to bring the Bush program within the rule of law: what to do with the so-called “third category” of detainees—suspects who may be difficult to convict under the American standards of justice, but who may pose a palpable threat if released.

Depending upon how many such “hard cases” exist, Craig says, the Administration will decide whether new laws, including possibly those enabling some sort of preventive detention, are necessary. Although the detainees from the Bush era pose the most immediate problem, he said, it’s possible that the new Administration may also want to handle future prisoners outside the existing criminal- and military-court system. “A good deal of policy research remains,” he said. “The door was not left open by accident. Obama wants the freedom to hear the recommendations of the most experienced and smartest people, on how to protect the American people while still respecting the rules of the road on liberty.” He suggested that the Administration would prefer not to go in that direction. “It’s possible but hard to imagine Barack Obama as the first President of the United States to introduce a preventive-detention law,” Craig said. “Our presumption is that there is no need to create a whole new system. Our system is very capable.” Then again, the idea is not being ruled out, which may be surprising to some constituents, given Obama’s past support for civil liberties and Craig’s own record—in the early nineties, he served as the chairman of the board of the International Human Rights Law Group, an advocacy organization now known as Global Rights.

Obama’s legal team is aware that every step it takes will be seen as an indication of core convictions. Craig, who will coördinate the revamping of the Bush Administration’s legal policies on terrorism, said, “One way we’ve looked at this is that we own the solution. We don’t own the problem—it was created by the previous Administration. But we’ll be held accountable for how we handle this.”

The Obama Administration has already inflamed some members of the human-rights community. On February 9th, the Justice Department adopted the same position that Bush had taken in a case filed by the American Civil Liberties Union. The government attempted to squelch a lawsuit initiated by a group of terrorist suspects—one of whom had allegedly been tortured in Morocco after being transferred there by the C.I.A.—on the ground that it would open up state secrets. Scott Horton, a law professor at Columbia University, characterized the new Justice Department’s position as a betrayal of the “promises of transparency and accountability” made by Obama during the campaign.

The first step in cases such as Marri’s, Craig suggests, will be to evaluate the “dangerousness” of each detainee, and to scrutinize all documents passed on by the previous Administration. “We need the facts,” he said. “And we need fresh eyes.” For years, John Ashcroft has justified the military detention of Marri as a safety precaution. “Sometimes the criminal courts are not up to it,” he told me. But, as the new team reviews Marri’s story, it will likely find ample grounds to reassess the notion that the courts can’t handle terror suspects, and that such suspects can’t be safely housed in the United States without incident.

In a recent interview, David Kelley, a former U.S. Attorney for the Southern District of New York, who supervised the early stages of the Marri case, revealed that he had warned his bosses in the Justice Department that they were making a mistake by sidestepping the criminal courts. Kelley co-chaired the Justice Department’s nationwide investigation into the 9/11 attacks, and headed the investigations into the 2000 attack on the U.S.S. Cole, in Yemen, and the 1998 bombings of the U.S. Embassies in Kenya and Tanzania; he also led the prosecution of Ramzi Yousef, in the 1993 World Trade Center bombing. In 2003, he successfully prosecuted John Walker Lindh, the American accused of aiding the Taliban. In the interview, Kelley said he believed that the government had a strong case against Marri: he had been charged with credit-card fraud, bank fraud, identity theft, and lying to a federal agent. He thought that Marri could be convicted in a matter of a few months, and sentenced to years in prison. Kelley, who is now a partner at Cahill Gordon, in Manhattan, was disappointed when, on the basis of a one-page executive order, Marri was suddenly sent to the brig. “My view is, we haven’t really exhausted the potential for using the criminal-justice system,” he said.

James Benjamin, a former federal prosecutor in the Southern District of New York, is now a partner at the law firm Akin Gump. In 2008, he co-wrote a review of the Marri case, characterizing the switch to military detention as counterproductive. “Definitely, the criminal-justice system can handle someone like Marri,” he told me. “They caught him under the criminal-justice system. And, based on what we know, they were poised to convict him.” What happened to Marri before he was moved “proves the system was up to it.”

Marty Lederman, a former Georgetown Law professor, whom Obama has appointed to be a deputy in the Justice Department’s Office of Legal Counsel, argues that the Bush Administration’s claims to be acting out of necessity were “nonsense.” In an essay published before he joined the Administration, Lederman wrote, “Even if everything the government alleges about al-Marri’s ties to al Qaeda are true,” he was not a danger “because he was already incapacitated—imprisoned—within the criminal-justice system, where his trial was pending.”

Marri had aroused the suspicion of law-enforcement officers almost as soon as he arrived in the Midwest with his wife, Maha, who spoke no English, and their five young children. His timing was conspicuous—he arrived in Chicago the day before 9/11. The next day, the family took a hundred-and-fifty-mile taxi ride to Peoria.

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Marri enrolled in computer-science classes at Bradley University, where he and a brother had obtained undergraduate degrees. Qatar, which has one of the highest per-capita incomes in the world, pays college tuition for many of its citizens, and several members of the Marri family have attended school in America. According to the Washington Post, as an undergraduate at Bradley Marri wore a ponytail and was known for his partying and his quick sense of humor. He returned to Qatar in 1991, after graduation. Later that decade, a palace coup in Qatar shook his family, eventually prompting some members to leave for Saudi Arabia, where many of his brothers and his wife now live. Marri reportedly ended up in Afghanistan. According to the sworn statement given by Jeffrey Rapp, the D.I.A. analyst, at some point between 1996 and 1998 Marri was trained in chemical weaponry at an Al Qaeda camp there. (Marri, through his lawyer, denied these allegations.)

Patrick Theros, who was the U.S. Ambassador to Qatar during this period, is skeptical of the terrorism allegations. “I’ve never heard anyone say this Qatari kid did anything,” he told me. Theros described Qatar as both religiously conservative and tolerant, and says that as far as he knows it is home to virtually no violent radical Islamic movements.

In the summer of 2000, Marri returned to Illinois, where he allegedly registered a carpet business in Macomb, and opened multiple bank accounts, under a false name and Social Security number. When he went back in the fall of 2001, according to the Washington Post, he had a briefcase filled with hundred-dollar bills. Rapp’s statement claims that Marri had obtained more than thirteen thousand dollars in cash from Mustafa Ahmed al-Hawsawi, the financier in the United Arab Emirates who is known to have bankrolled the September 11th hijackers. Phone records apparently offered further evidence of a tie between Marri and Hawsawi.

Law-enforcement authorities pieced together this picture bit by bit. In September, according to the Post, local police stopped Marri while he was driving, checked his license, and discovered an outstanding warrant for drunken driving, dating back to his earlier student days, as well as the briefcase filled with cash. The police notified the F.B.I. Several weeks later, his lawyers say, a cell-phone salesman, noting discrepancies in Marri’s identification documents, also called the bureau. In October and December, 2001, F.B.I. agents interviewed Marri; they say that he offered to let them search his laptop computer, his minivan, and his small rental apartment. Later, Marri’s lawyers argued that the agents had failed to obtain a warrant, and that the information from the search could therefore not be admitted into evidence. According to Rapp’s statement, Marri’s computer was filled with information on deadly poisons, including a step-by-step guide to making hydrogen cyanide—a toxic substance that can be used in poison-gas attacks. Marri, in claiming his innocence, has had no chance to see the evidence against him. Asked recently why he was researching such chemicals, Marri, through his lawyers, gave his first public answer. He was “doing research for a family member in the petrochemical industry to be used for industrial purposes. The research involved visiting Web sites that contained hundreds of nonpoisonous chemicals (not just cyanide). And even cyanide has numerous industrial uses.”

The laptop also reportedly contained lectures by bin Laden, and unsent e-mails to an address that Rapp said was connected to Khalid Sheikh Mohammed. Some of Marri’s e-mails were encoded. Upon discovering this information in his laptop, the F.B.I. arrested Marri as a material witness to its investigation of the attacks. Soon after, he was charged with credit-card fraud and with failing to tell the F.B.I. about his 2000 visit to America and his phone calls to Hawsawi.

On the morning of June 23, 2003, only days before Marri’s defense team was to make its arguments about suppressing the laptop and other evidence, one of his lawyers received a phone call informing him that a U.S. Attorney would be making an unexpected appearance at the courthouse that day. President Bush, the lawyers soon learned, had signed an executive order directing the military to seize Marri. “We should have seen it for what it was—the foreshadowing of an Administration that was going to forsake the Constitution in the war on terror,” Lawrence Lustberg, one of the earliest defense lawyers on what has come to be Marri’s team, said. “From then on, we didn’t see Marri or hear from him again until late 2004. He just went into the abyss.”

Before agreeing to transfer Marri to the brig, however, the presiding judge in the case ruled that the White House would be barred from charging Marri again with the same crimes. In legal jargon, the original charges were “dismissed with prejudice,” to protect Marri’s right not to be placed in “double jeopardy.” As a result, if the Obama Administration decides to charge him in the criminal system now, it has to bring a different set of charges, unless Marri’s lawyers offer a deal. Benjamin, the former prosecutor, insists that “there is a whole bag of tools for dealing with truly bad guys—there are many other statutes that the government could explore, including material support of terrorism, conspiracy charges, and mail- and wire-fraud charges.” But, he suggests, by taking Marri outside the regular criminal system “there’s no doubt they made all kinds of problems for themselves.”

Andrew McCarthy, a former federal terrorism prosecutor who writes for National Review, defends Marri’s transfer to the brig. “Sure, the criminal-justice system, by permitting Marri’s pretrial detention, neutralized him, at least for a time,” he says. “But there’s always the chance the court will release a defendant on bail.” Moreover, he argues that open criminal trials run many risks, including the accidental, or oblique, disclosure of classified information. It’s also unclear how to handle witnesses who may themselves be terrorists: they may demand immunity before they will talk. Or it may be that their testimony was obtained by unsavory means, which could scuttle a conviction.

In the Marri case, however, it does not appear that a fear of losing led Bush to transfer him to the Navy brig. Kelley, for example, thought that the case the government had was “solid.” Instead, it appears that the real motive was frustration on the part of the Justice Department at being unable to make Marri confess. Kelley was told to push him hard, which he did, but Marri kept professing his innocence. As Ashcroft wrote in his 2006 book about fighting terrorism, “Never Again,” “Al-Marri rejected numerous offers to improve his lot by cooperating with the F.B.I. investigators and providing information. He insisted on becoming a ‘hard case.’ ” Mark Berman, an early member of Marri’s defense team, asserts that the Bush Administration “really just wanted to interrogate him” in a rough manner. “No doubt about it.”

The right to remain silent is a fundamental aspect of the American justice system. Justice John Paul Stevens, dissenting in the 2004 case Rumsfeld v. Padilla, wrote, “Executive detention of subversive citizens, like detention of enemy soldiers to keep them off the battlefield, may sometimes be justified to prevent persons from launching or becoming missiles of destruction. It may not, however, be justified by the naked interest in using unlawful procedures to extract information. Incommunicado detention for months on end is such a procedure.… For if this Nation is to remain true to the ideals symbolized by its flag, it must not wield the tools of tyrants even to resist an assault by the forces of tyranny.”

The summer of 2003, when Marri entered the brig, was the height of the Bush Administration’s program of authorized abusive interrogations. The C.I.A. had just taken Khalid Sheikh Mohammed into custody, and was using extreme measures to make him divulge information (much of which he later recanted). Marri was among those whom Mohammed apparently implicated during this period. By then, Bush appointees in the Justice Department had produced numerous memos advising the C.I.A. and the Pentagon that there were virtually no legal impediments to the use of physical and psychological force to break “unlawful enemy combatants.” Suspects considered especially “high value” were subjected to extreme sensory deprivation and other harsh tactics, which were modelled on Soviet and Chinese torture programs that had been studied and copied by the C.I.A.

Inside the Charleston brig, documents show, officials were ordered to follow the same rules as those at Guantánamo. Lustberg, however, says, “I’ve been to Guantánamo. Marri was far more isolated. He had no contact with any other detainees. Most days, he had no human contact at all.”

For the first six months, Marri was kept in an eight-foot-by-ten-foot cell with one blacked-out window, no social interaction, and nothing to do or to read. An internal report, declassified in 2005, showed that during this period the Department of Defense ordered the removal of the mattress, pillow, and Koran of a detainee in the brig. Marri was also deprived of visits from the Red Cross, in violation of international laws. He was denied hot food, and consistently felt cold: he was given no socks, and his bed had only a stiff “anti-suicide” blanket—one that cannot be made into a noose. Andrew Savage, the local counsel for Marri in Charleston, says, “It was a psychological effort to devalue him. He was going crazy. He thought the smells from the nearby paper mill were poisoning him.” At other points, Marri started feeling “tingles” all over, and began hallucinating that microphones had been installed in his cell. “He was getting delusional,” Savage said.