Holder’s choice of a civilian trial for the architect of 9/11 has galvanized Republicans.Illustration by Finn Graff

On December 5th, several hundred people gathered in Foley Square, in lower Manhattan, and withstood a drenching rainstorm for two hours in order to send a message to Attorney General Eric Holder. A JumboTron, set up by the protesters, played clips of Holder’s recent testimony before Congress, in which he explained his decision to hold the trial of Khalid Sheikh Mohammed—the self-proclaimed planner of the terrorist attacks of September 11, 2001—and four co-conspirators in the colonnaded federal courthouse flanking the square, rather than in a military commission at Guantánamo Bay, Cuba. Members of the crowd shouted at the screen: “Holder’s gotta go!”; “Arrogant bastard!”; “Communist!”

Greg Manning, whose wife, Laura, was severely burned in the World Trade Center attacks, stood before the crowd and said, “Thousands are already dead because of Khalid Sheikh Mohammed’s choices. We do not want to see . . . hundreds of thousands dead because of the Attorney General’s choices.”

Andrew McCarthy, the former Chief Assistant U.S. Attorney who led the prosecution of the 1993 World Trade Center attacks, also gave a speech, declaring that Holder didn’t “understand what rule of law has always been in wartime.” He said, “It’s military commissions. It’s not to wrap our enemies in our Bill of Rights.”

“Traitor!” someone shouted.

Edith Lutnick, who works for the Cantor Fitzgerald Relief Fund, told the crowd, “My brother, Gary, lost his life that day.” The 9/11 victims, she said, “were murdered by the terrorist Khalid Sheikh Mohammed, and we do not want him and his fellow-terrorists tried in that building. . . . We need to tell Eric Holder that we will be victims no more.”

“Lynch Holder!” an onlooker cried.

One protester, Carolyn Walton, who works for a water-filtration company in Manhattan, told me that Holder was “a Marxist mole.” She asked, “How can someone who is not an American have any right to our rights? Holder wants to help the terrorists.”

The rally was organized, in part, by Debra Burlingame, the sister of the pilot Charles Burlingame, who was killed on 9/11 when Al Qaeda hijackers crashed the plane he had been flying into the Pentagon. Burlingame is one of the three founders of Keep America Safe, a new political-advocacy group. Her partners in the venture, which is aimed at attacking the Obama Administration’s national-security decisions and vindicating those of the Bush Administration, are William Kristol, the conservative pundit, and Elizabeth Cheney, the daughter of former Vice-President Dick Cheney. The organization’s political strategist is Michael Goldfarb, a spokesman for Senator John McCain during his 2008 Presidential campaign; among its funders is Mel Sembler, a conservative donor and a former finance chairman of the Republican National Committee.

Despite the prominence of the demonstration’s organizers, the campaign against Holder’s Justice Department was largely overlooked by the national media, which considered the event a fringe affair. But the anger was growing, and it became impossible to ignore on January 19th, when Scott Brown, a Republican, captured the Senate seat left vacant by the death of Edward Kennedy, the Massachusetts Democrat. As Eric Fehrnstrom, Brown’s political consultant, put it to me recently, the “most potent political issue” in the race was voter opposition to the Justice Department’s decision to extend customary legal protections to suspected terrorists such as Khalid Sheikh Mohammed and Umar Farouk Abdulmutallab, the Nigerian suspect who on Christmas Day attempted to detonate a bomb on a Northwest Airlines passenger plane bound for Detroit. In a debate with his Democratic opponent, Martha Coakley, Brown declared, “We’re at war in our airports, we’re at war in our shopping malls. I have to be honest with you, folks. . . . I’m scared at some of the policies I’ve heard.”

In a television ad, Brown, who is in the Army National Guard, flashed a photograph of himself in fatigues and declared, “Some people believe our Constitution exists to grant rights to terrorists who want to harm us. I disagree.” Brown also announced his support for waterboarding suspected terrorists—a tactic that Holder, among others, has denounced as torture. As Brown’s attacks grew more pointed, Fehrnstrom said, Coakley got “bollixed up” defending Obama’s policies. He added, “The obvious follow-up is: Are you going to read Osama bin Laden the Miranda warning if you catch him?”

After the Christmas Day incident, conservative pundits lambasted the Justice Department’s handling of Abdulmutallab, who had concealed in his underwear a bomb that ignited but failed to explode. When the plane landed, Abdulmutallab was taken to a hospital for treatment; at Holder’s directive, he was arrested as a criminal suspect. (The F.B.I., the C.I.A., and the Pentagon signed off on Holder’s decision.) F.B.I. agents questioned Abdulmutallab for some fifty minutes, under what is known as the “public-safety exception” to the right to remain silent. He divulged time-sensitive intelligence: he had been trained in Yemen, by affiliates of Al Qaeda, and had obtained explosives from them. After he received medical treatment, a Justice Department source said, he started to “act like a jihadi and recite the Koran.” He stopped coöperating and demanded a lawyer, at which point authorities read him his rights. On “Inside Washington,” Charles Krauthammer declared that it was “almost criminal” that Holder had allowed Abdulmutallab access to an attorney. Rudy Giuliani, the former mayor of New York, appeared on ABC, saying, “Why in God’s name would you stop questioning a terrorist?”

Joseph Lieberman, the Independent senator from Connecticut, released a statement declaring that Abdulmutallab was “an enemy combatant and should be detained, interrogated, and ultimately charged as such.” Then, to the dismay of Justice Department officials, the Obama Administration’s top intelligence official, Dennis Blair, the director of National Intelligence, appeared at a Senate hearing and, under harsh questioning from Republicans, second-guessed Holder’s decision to turn Abdulmutallab over to the F.B.I. (Blair later said that his remarks had been “misconstrued.”) Soon, even Democrats were attacking Holder’s decisions. In a letter to Obama, Dianne Feinstein, the chair of the Senate Intelligence Committee, suggested that holding a trial in New York was dangerous. “New York City has been a high-priority target since at least the first World Trade Center bombing,” she wrote. “The trial of the most significant terrorist in custody would add to the threat.”

The death blow was struck by New York’s mayor, Michael Bloomberg, who had previously pledged his support to Holder. On January 27th, Bloomberg distanced himself from the Justice Department, saying that a trial in New York would be too expensive. For months, companies with downtown real-estate interests had been lobbying to stop the trial. Raymond Kelly, the commissioner of the New York Police Department, had fortified their arguments by providing upwardly spiralling estimates of the costs, which the federal government had promised to cover. In a matter of weeks, in what an Obama Administration official called a “classic City Hall jam job,” the police department’s projection of the trial costs went from a few hundred million dollars to a billion dollars.

Senator Charles Schumer, of New York, quickly released a statement echoing Bloomberg; the wisdom of moving the trial away from lower Manhattan, he said, was “obvious.” Then, on February 1st, Schumer told the Daily News that he opposed the idea of a 9/11 trial taking place anywhere in New York State. Officials in Pennsylvania and Virginia—the two other states where the 9/11 attacks occurred—began declaring their opposition to hosting the trials, too.

Bill Martel, an international-security expert at the Fletcher School, at Tufts University, told me that Holder, having been impervious to the shifting public mood, had been sucked into “a political riptide.” The Christmas Day bombing attempt, he noted, had come only a month after Nidal Malik Hasan, an Army psychiatrist who had exchanged e-mails with radical Islamists, massacred thirteen people at Fort Hood, Texas. Both incidents had revived public concern about America’s vulnerability to terrorism. Holder’s decisions, Martel warned, had “the makings of a sustained and self-inflicted political hemorrhage.” He added, “I think they’re going to have to give up on civilian trials. And Eric Holder is in for some pretty brutal days.” Indeed, on January 31st, Senator Lamar Alexander, of Tennessee, declared on Fox News that Holder should “step down,” for his inability to make “a distinction” between “terrorists who are flying into Detroit, blowing up planes, and American citizens who are committing a crime.”

On January 11th, a few weeks before his plans for a trial at Foley Square fell apart, Holder flew to Boston, to preside over the installation of a new U.S. Attorney. That evening, he returned to Washington in the Justice Department’s Gulfstream jet. Holder, who had jokingly lamented that such perks wouldn’t last forever—“I’m missing it already!”—sat down, put on headphones, and blasted one of his favorite songs, Jimi Hendrix’s “Purple Haze.” Holder, who is fifty-nine, seemed determined not to let the tensions of Washington politics poison his mood. He was equally determined not to capitulate on the idea of holding a 9/11 trial. “I don’t apologize for what I’ve done,” he told me at one point. “History will show that the decisions we’ve made are the right ones.” Holder said that he regarded trying Khalid Sheikh Mohammed in a courtroom as “the defining event of my time as Attorney General.” But, he added, “between now and then I suspect we’re in for some interesting times.”

Holder, despite the controversy he has inspired, has not actually pushed for radical change. Indeed, critics in left-leaning legal circles have complained that he has kept too many of George W. Bush’s counterterrorism policies in place. For example, Holder’s Justice Department has continued blocking lawsuits by people who were subjected to extraordinary rendition—the practice of sending suspected terrorists captured abroad to countries known for administering torture—on the ground that such litigation would expose state secrets. Even some former members of the Bush Administration see more continuity than change. Bradford Berenson, who served as a White House lawyer when the Bush Administration was forging its controversial legal approach to terrorism, told me that “from the perspective of a hawkish Bush national-security person the glass is eighty-five per cent full in terms of continuity.”

Holder told me that he was frustrated by much of the criticism over the handling of Abdulmutallab. “What we did is totally consistent with what has happened in every similar case” since 9/11, he said. “There’s a desire to ignore the facts to try to score political points. It’s a little shocking.” Without exception, he noted, every previous terrorist suspect apprehended inside the country had been handled as a civilian criminal. Even so, critics such as Krauthammer were denouncing Holder for failing to send Abdulmutallab directly to Guantánamo. As a senior national-security official in the White House put it, “It’s a fantasy! Under what alternative legal system can Special Operations Forces fly into Detroit, and take someone away without court oversight?”

According to Kate Martin, the director of the Center for National Security Studies, in Washington, the military can’t simply grab suspects inside the U.S. and hold them without charge or a hearing. “It violates the Constitution, which extends to everyone inside the U.S.,” she said. “You can’t be seized without probable cause. You have the right to due process, and to a trial by a jury of your peers—which a military commission is not.” Confusion on this point may derive from the Bush Administration’s controversial handling of two suspected terrorists, José Padilla and Ali Saleh Kahlah al-Marri. Both men were arrested in the U.S. by law-enforcement officials, and indicted on criminal charges. But Bush declared Padilla and Marri to be “enemy combatants,” which, he argued, meant that they could be transferred to military custody, for interrogation and detention without trial. (Neither suspect provided useful intelligence.) The cases provoked legal challenges, and in both instances appeals courts ruled that Bush had overstepped his power. The Administration, not willing to risk a Supreme Court defeat, returned the suspects to the civilian system.

For all the tough rhetoric of the Bush Administration, it prosecuted many more terror suspects as criminals than as enemy combatants. According to statistics compiled by New York University’s Center on Law and Security, since 2001 the criminal courts have convicted some hundred and fifty suspects on terrorism charges. Only three detainees—all of whom were apprehended abroad—were convicted in military commissions at Guantánamo. The makeshift military-commission system set up by Bush to handle terrorism cases has never tried a murder case, let alone one as complex, or notorious, as that of Khalid Sheikh Mohammed, who will face the death penalty for the murder of nearly three thousand people.

The Bush Administration obtained life sentences in the criminal courts for two terror suspects arrested inside the U.S.: Richard Reid, the so-called shoe bomber, and Zacarias Moussaoui, who was planning a second wave of plane attacks. (Reid was read his Miranda rights four times.) When the Bush Justice Department obtained these convictions, the process was celebrated by some of the same people now criticizing Holder. Giuliani, after the Moussaoui trial, said, “I was in awe of our system. It does demonstrate that we can give people a fair trial.”

Holder told me that he was “distressed” that people “who know better” were claiming that the courts were not up to the job of trying terrorists. He added that he found it “exceedingly strange” to hear this argument from Giuliani, who had been a zealous prosecutor. “If Giuliani was still the U.S. Attorney in New York, my guess is that, by now, I would already have gotten ten phone calls from him telling me why these cases needed to be tried not only in civilian court but at Foley Square,” Holder said.

There is no evidence suggesting that military commissions would be tougher on suspected terrorists than criminal courts would. Of the three cases adjudicated at Guantánamo, one defendant received a life sentence after boycotting his own trial; another served only six months, in addition to the time he had already served at the detention camp; the third struck a plea bargain and received just nine months. The latter two defendants—Salim Hamdan, a Yemeni who worked as Osama bin Laden’s driver, and David Hicks, an Australian who attended an Al Qaeda training camp—are now at liberty in their home countries, having been released while Bush was still in office. It’s impossible to know how these same cases would have fared in the civilian system. But the case of John Walker Lindh, the so-called American Taliban, offers a comparison between the two systems, as it closely parallels the case of Yaser Hamdi, a Saudi-American who was captured in the same place (Afghanistan) and at the same time (2001). Lindh, who pleaded guilty in a criminal court, is now serving twenty years in prison. Hamdi, who was declared an enemy combatant, was held in military detention, without charge; in 2004, after a court challenge, he was freed, and is now in Saudi Arabia.

“Let me guess—your gas pedal stuck.”

Michael Mukasey, who was Holder’s predecessor as Attorney General, has suggested that the military system is better at making terrorists talk. Last month, in the Wall Street Journal, he argued, “Had Abdulmutallab been turned over immediately to interrogators intent on gathering intelligence, valuable facts could have been gathered and perhaps acted upon.” But the conventional court system has proved surprisingly effective at extracting intelligence. Dozens of suspected terrorists in the criminal system have coöperated with the government, usually in exchange for leniency in sentencing. The government is currently receiving valuable information from David C. Headley, who was indicted last December, in Chicago, for his involvement in terrorism conspiracies in India and Denmark. And, last week, the Justice Department confirmed that Abdulmutallab was now coöperating with the F.B.I. A department official noted, “He has an incentive to talk in the criminal-justice system, which the other system doesn’t offer.” The key to gaining Abdulmutallab’s coöperation was the F.B.I.’s ability to enlist his family in getting him to talk. Holder asked me, “Would that father have gone to American authorities if he knew his son might be whisked away to a black site”—a secret prison set up in a foreign country—“and subjected to enhanced interrogation techniques? You are much more likely to get people coöperating with us if their belief is that we are acting in a way that is consistent with American values.”

On January 13th, Holder discussed the controversies surrounding him, in a conference room on the top floor of the Justice Department building. The walls were hung with portraits, which Holder had chosen, of his favorite Attorneys General. One was of Elliott Richardson, who resigned rather than follow President Richard Nixon’s demand that he halt the Watergate investigation.

Some of Holder’s friends, who call him Mr. Nice Guy, wonder if he is as tough as some of these predecessors. “Attorneys General should be feared,” one legal observer told me. “They have incredible power. Holder makes correct decisions on the law, but he’s not aggressive.” Holder bristles at such characterizations. His Secret Service code name is Fidelity, but he joked, “I’d like something like The Hammer.”

Though Holder has improved the morale at the Justice Department, he has had some management difficulties. He did not get along with David Ogden, his deputy. Ogden announced his decision to resign last December,** and has not been replaced. A lawyer who is close to the Administration said, “Eric’s weakness is his management skills, but his strength is his gut.”

Holder tried to address his critics with lawyerly detachment. Dick Cheney had equated Holder’s approach to handling terrorism with giving “aid and comfort to the enemy”—the legal definition of treason. Holder said of Cheney, “On some level, and I’m not sure why, he lacks confidence in the American system of justice.” He added that he had seen documents making clear that Cheney’s office was the driving force behind the Bush Administration’s most controversial counterterrorism policies, especially those sanctioning brutal interrogations. He said of Cheney, “I think he’s worried about what history’s judgment will be of the role that he played in making decisions about everything from black sites to enhanced interrogation techniques.” Holder said that he doesn’t know Elizabeth Cheney, but noted, with a laugh, “She’s clearly her father’s daughter.”

Holder shook his head at Scott Brown’s assertion that America’s “laws are meant to protect this nation, not our enemies.” Such rhetoric, he said, was “inconsistent with a little organization called the United States Supreme Court.” During the Bush years, U.S. courts consistently struck down claims that detainees at Guantánamo, including Khalid Sheikh Mohammed, were beyond the reach of U.S. and international law. Moreover, Guantánamo detainees receive legal counsel that is paid for by the U.S. government. Holder said, “It’s distressing to me that on an issue that is truly a matter of life and death for this nation people will find a way to make that a partisan issue.”

Despite such comments, Holder is not naïve. He has spent almost his entire career in the public arena, most of it at the Justice Department. After graduating from Columbia Law School, in 1976, he became a prosecutor in the department’s public-integrity section, going after lawbreakers in both parties. In 1988, President Ronald Reagan appointed him to the Superior Court in Washington. Five years later, President Bill Clinton appointed him the District of Columbia’s U.S. Attorney; he was the first African-American to hold the post. In 1997, he became Deputy Attorney General, under Janet Reno. Holder was a lifeline at the Justice Department for Rahm Emanuel, then a senior White House adviser, because communications were so strained between Clinton and Reno, over such issues as her appointment of an independent counsel to investigate the Monica Lewinsky scandal.

In 2001, Holder himself was embroiled in a scandal, for having supported Clinton’s last-minute pardon of the financier Marc Rich, who had fled the country rather than face criminal charges; his ex-wife, Denise, was a Presidential friend and fund-raiser. Holder never consulted with the prosecutors in the case, infuriating them. Afterward, many of Holder’s friends suspected that he had let his desire to ingratiate himself with Clinton override what one of them called “that gnawing uneasiness.” Holder’s actions have not been forgotten. Andrew McCarthy, the former federal prosecutor, said, “He had a background going into this that would have made him unconfirmable if he was a Republican.” Holder emerged from the scandal, a friend said, determined to appear that he was above politics. “After being accused of not standing up to that kind of pressure, he’s establishing his independence,” the friend said. “It all goes back to Marc Rich.”

As Attorney General, Holder has tried to depoliticize one of the most polarizing issues facing the Administration: how to protect the country from terrorism. David Vladeck, a former law-school classmate, who is now the director of the Bureau of Consumer Protection, said, “His vision as Attorney General is to be seen as a lawyer, and to get away from what was a partisan-infected Justice Department. He doesn’t want to be Ed Meese or John Ashcroft. He doesn’t want the Justice Department to be seen as another political agency. He’s sent the unmistakable message to the people at D.O.J. that after years of politicization they are now going to do the right things, regardless of politics.”

Karen Greenberg, the executive director of the Center on Law and Security, said that a difficulty with recalibrating what was formerly called the “war on terror”—a term that Obama has shunned—is that any change is seen as “a slap in the face of all that Bush did.” She added, “The Justice Department was emasculated under Bush. Holder’s trying to reassert its lead role in handling the prosecution of terrorism, which Bush delegated to the Pentagon. It’s not minor. It’s about bringing the whole approach to handling terrorists back inside the rule of law. But it’s a public rebuke, suggesting that for eight years his predecessors betrayed American traditions.” This is especially true in the case of Khalid Sheikh Mohammed, for Holder is explicitly overriding the Bush Administration’s judgment that the case belongs in a military commission at Guantánamo.

As a result, it is proving virtually impossible for Holder to make mid-course legal corrections without sparking political fights over the Bush legacy. Many of Obama’s political advisers see such battles as exactly the kind of “wedge” issues that alienate the independent voters they need. So far, polls show that the President has repaired the Democrats’ image problem on national-security issues; his approval rating on handling terrorism is about fifty per cent, and was unhurt by the Christmas Day fracas. The one national-security policy on which recent public-opinion polls register extreme disapproval is the decision to handle terror suspects as civilian criminals.

Holder’s unpopular positions on terrorism issues have frustrated Obama’s advisers. The lawyer close to the Administration said, “The White House doesn’t trust his judgment, and doesn’t think he’s mindful enough of all the things he should be,” such as protecting the President from political fallout. “They think he wants to protect his own image, and to make himself untouchable politically, the way Reno did, by doing the righteous thing.” On November 13th, when Holder announced his plan to try the 9/11 defendants in New York, Obama was travelling in Asia. He told reporters there, “We have to break . . . this fearful notion that somehow our justice system can’t handle these guys.” But as political tensions mount it’s unclear how far the White House will go to back Holder. Greg Craig, Obama’s first White House counsel, resigned under pressure in January, after clashing with Rahm Emanuel, the White House chief of staff, over his attempts to reverse Bush Administration counterterrorism policies.

Holder told me that he has no doubt that Obama supports him. They have shared some private moments. Late last year, Holder accompanied Obama on a middle-of-the-night visit to Dover Air Force Base. An Air Force plane had just delivered eighteen bodies of soldiers and Drug Enforcement Administration officials who had been killed that week, in Afghanistan. Holder said that Obama, after seeing a hangar filled with caskets, sat alone in a nearby room. Holder added that he “was struck by the fact that this guy has the weight of the world on his narrow shoulders.”

On January 5th, Obama held a national-security meeting in the White House Situation Room to review how the Administration had failed to detect and prevent the Christmas Day plot. Afterward, Holder said, Obama asked him to walk back to the Oval Office with him. “We talk about these matters,” Holder said. “The decisions are, relatively, mine. I take responsibility for them. But these are things where he is kept in the loop, and the direction he gives obviously has to be factored into any decision I make.” Holder declined to reveal details of their recent discussion but said, “We are on the same page.” He added, “He recognizes that being Attorney General at this time is not the easiest job in the world.”

When Holder announced, last November, his decision to try Mohammed and his co-conspirators in a federal courthouse, he predicted that it would be “the trial of the century.” It had taken him months to arrive at the best way to bring Mohammed to justice. By the time he became Attorney General, the Bush Administration had moved Mohammed—whom the C.I.A. took into custody seven years ago, in Pakistan—from a black-site prison to Guantánamo. His prosecution was complicated by the fact that C.I.A. interrogators had subjected him to torture, including at least a hundred and eighty-three sessions of waterboarding.

Bush Administration officials, too, had recognized Mohammed’s abuse as an impediment to prosecution. After Mohammed arrived at Guantánamo, a team of F.B.I. and military interrogators tried to elicit from him and his co-defendants the same confessions that the C.I.A. had obtained about the 9/11 plot, but by using only legal means of interrogation. (According to the Washington Post, he was enticed with Starbucks coffee.) By 2008, the Bush Administration believed that this so-called Clean Team had compiled sufficient evidence to charge Mohammed and the others with capital murder. The cases were to be tried in military commissions, which have more lenient rules of evidence than civilian courts. But even in this forum, several outside experts warned, the Administration might have trouble using any evidence that had originally been obtained with methods that would “shock the conscience of the court.” John D. Hutson, a former judge advocate general, told the Washington Post that “there’s something in American jurisprudence called ‘fruit of the poisonous tree.’ You can clean up the tree a little, but it’s hard to do.”

In December, 2008, Mohammed and his co-defendants cast further legal uncertainty over the proceedings at Guantánamo by insisting that they preferred to plead guilty without a trial, and be put to death as “martyrs.” The defense counsel for two of the defendants protested that their clients were not competent to make such a decision. The cases stalled while psychological evaluations took place.

Amid this legal tumult, Obama assumed the Presidency. Days after taking office, he signed executive orders suspending the military commissions at Guantánamo, and calling for the closure of the detention facility within a year. He vowed to end legal abuses that had made Guantánamo infamous, such as indefinite detention without credible judicial review. He also banned torture and other cruel forms of interrogation, and foreclosed the option of detaining terror suspects in black sites. (Some of these practices had already been suspended by Bush, in the face of court orders and public disapproval.)

In January, 2009, there was bipartisan support for closing down Guantánamo, including from John McCain and from President Bush himself, who had said, “I’d like it to be over with.” General Colin Powell, Bush’s former Secretary of State, had declared, “If it was up to me, I would close Guantánamo not tomorrow but this afternoon.” Robert Gates, Bush’s Secretary of Defense, whom Obama asked to stay on, had already considered a plan to transfer the remaining two hundred and sixty-five detainees—including Mohammed—to America. A former Pentagon official told me that the plan, which never surfaced publicly, called for the prisoners to be held in the Navy brig in Charleston, South Carolina. (Geoff Morrell, a Pentagon spokesman, said, “The plan never left the building.”)

Holder had been an outspoken critic of Bush’s terrorism policies. In 2008, he gave a speech to the American Constitution Society, and described some of the steps Bush had taken as “excessive and unlawful.” He said, “We owe the American people a reckoning.”

Obama’s executive orders effectively put Holder in charge of the legal process of closing Guantánamo. Most of the President’s legal advisers believed that virtually all the Guantánamo detainees could be tried in criminal courts, or transferred to courts in other countries. Amy Jeffress, Holder’s national-security adviser, set up three interagency task forces to review the detainees’ cases. But the challenge proved far greater than expected. “There was no file for each detainee,” Jeffress told me. “The information was scattered all over the government. You’d look at what the Department of Defense had, and it was something, but, as a prosecutor, it wasn’t what you’d like to see as evidence. . . . It was pretty thin stuff.” The Bush Administration, she said, clearly “hadn’t planned on prosecuting anyone. Instead, it was ‘Let’s take a shortcut and put them in Guantánamo.’ ”

In a speech last May, Obama declared that the Bush Administration’s legal approach had created “a mess.” Among other problems, Obama’s Justice Department found itself under frequent attack in the courts for Bush-era policies. Detainees were winning habeas-corpus hearings, and public-interest groups were mounting challenges to the Bush Administration’s stances on state secrecy, surveillance, and torture. In addition, the Obama Administration faced litigation over access to Bush-era documents. An informed source said of the situation, “We were buried in an avalanche of shit.”

Holder set up an elaborate review process for detainees. On Wednesday afternoons, twenty senior government officials from the defense, intelligence, legal, and foreign-policy bureaucracies met for hours in a secure, undisclosed location, to weigh the case of each prisoner at Guantánamo. Sometimes they spent weeks on just one case. Ambassador Daniel Fried, who was appointed by Obama to manage the closure of Guantánamo, and who served in the Bush Administration, told me that the process was “remarkably effective,” but hovering in the background was the fear of making a lethal mistake. A member of the detainee task force said, “It’s like the parole board. Do this long enough, and you’ll have a Willie Horton.” But, Fried said, “the damage done by Guantánamo was greater than the damage done by some of the low-level people let out.” Also great, he believed, was the cost of trying suspects in military hearings that much of the world considered illegitimate. As the man in charge of persuading other countries to accept Guantánamo detainees, he noted that “Holder’s decision to try the 9/11 defendants in the courts has made my job a lot easier.”

“Got any bathtub gin?”

Officials at the White House would not say the same. Last spring, a series of Justice Department moves prompted attacks from Republicans, causing concern in what’s known as the White House “front office,” where Emanuel and David Axelrod, Obama’s top political adviser, work. Most notably, the detainee task force recommended the release of two Guantánamo detainees in America. The recommendation received unanimous support from the principals committee of the National Security Council. Among those who signed off were Holder and the Cabinet secretaries dealing with defense, intelligence, foreign affairs, and homeland security. The two detainees were Chinese Uighurs whom the courts had ordered to be set free, after the Bush Administration had conceded that they were not enemy combatants. But the government had been unable to find any country willing to take them except China, where, as dissidents, they would be jailed.

Lawyers in the Homeland Security and Justice Departments, along with the Uighurs’ attorneys, formed a plan to resettle the men in northern Virginia. But the White House front office saw the release as politically toxic, and stood in its way. In May, word of the secret plan leaked, causing Republicans in Congress to declare their opposition to bringing any detainees to the U.S. At a White House meeting, Obama suggested that he had been blindsided by the Uighur plan, and that he disapproved of it.

Within days, both the House and the Senate had voted to strip a spending bill of eighty million dollars that had been requested for the closing of Guantánamo. Last fall, Congress passed legislation barring the government from bringing any detainee from Guantánamo to America, except to stand trial. Elisa Massimino, the president of Human Rights First, told me, “Politically, these issues are poisonous. That’s what Rahm Emanuel is looking at.” But, she added, “You can’t finesse it, and you can’t spin it. The President just has to lead the American people away from fear.”

Emanuel viewed many of the legal problems that Craig and Holder were immersed in as distractions. “When Guantánamo walked in the door, Rahm walked out,” the informed source said. Holder and Emanuel had been collegial since their Clinton Administration days. Holder’s wife, Sharon Malone, an obstetrician, had delivered one of Emanuel’s children. But Emanuel adamantly opposed a number of Holder’s decisions, including one that widened the scope of a special counsel who had begun investigating the C.I.A.’s interrogation program. Bush had appointed the special counsel, John Durham, to assess whether the C.I.A. had obstructed justice when it destroyed videotapes documenting waterboarding sessions. Holder authorized Durham to determine whether the agency’s abuse of detainees had itself violated laws. Emanuel worried that such investigations would alienate the intelligence community. But Holder, who had studied law at Columbia with Telford Taylor, the chief American prosecutor in the Nuremberg trials, was profoundly upset after seeing classified documents explicitly describing C.I.A. prisoner abuse. The United Nations Convention Against Torture requires the U.S. to investigate credible torture allegations. Holder felt that, as the top law-enforcement officer in the U.S., he had to do something.

Emanuel couldn’t complain directly to Holder without violating strictures against political interference in prosecutorial decisions. But he conveyed his unhappiness to Holder indirectly, two sources said. Emanuel demanded, “Didn’t he get the memo that we’re not re-litigating the past?”

Last spring, under pressure from the defense establishment, Obama decided to reform the military commissions rather than terminate them, to the disappointment of his liberal base. A protocol was drafted, directing the Pentagon and the Justice Department to work together in settling turf battles. The presumption, the draft said, was that detainees should be tried in civilian courts unless there were compelling reasons not to do so. Holder was put in charge of deciding which legal system was appropriate for each Guantánamo detainee.

Some legal experts regarded the process as odd, since it removed the President from taking the lead role. Philip Bobbitt, a law professor who served in the National Security Council under Clinton, said the protocol made Obama “look as if he’s not in charge.” A government official involved in the process told me, “My sense is that Obama wanted the Attorney General to make the call.”

Last July, Holder assigned eight experienced criminal prosecutors from the Southern District of New York and the Eastern District of Virginia to build the best criminal case they could against Mohammed and his co-conspirators. They had until October 1st to investigate. The prosecutors gathered fresh evidence from around the globe, rendering the military’s case comparatively weak. Neil MacBride, the U.S. Attorney who represents Virginia’s Eastern District, participated in the process, and said, “The prosecutors came together, and produced hundreds of pages of analysis that was granular, and evidence-specific.” Many countries that had refused to coöperate with military commissions at Guantánamo were much more favorably disposed to criminal trials. Among the countries that stood willing to provide evidence and witnesses for court prosecutions were Germany, France, and Great Britain.

In weighing the cases of Mohammed and his co-conspirators, Holder conferred with top Pentagon lawyers, including Jeh Johnson, the Defense Department’s general counsel, and William Lynn, the Pentagon’s head of detainee affairs. The Pentagon’s prosecutors were initially reluctant to relinquish the cases, but in the end supported the decision. Holder then picked the Pentagon to prosecute five key suspects in the bombing of the U.S.S. Cole, a Navy ship attacked in Yemen by Al Qaeda in 2000. Sarah Mendelson, a director at the Center for Strategic and International Studies, in Washington, followed the deliberations closely, and told me, “You could see Holder negotiating.”

Holder, MacBride said, also conferred with his counterparts in the intelligence community about any possible jeopardy to national-security secrets “if we went forward with a full-throated prosecution of K.S.M.” Critics have raised worries that an open trial, which would require the government to reveal the names of witnesses and sources of evidence, could tip off enemies of the U.S. about sensitive security matters. A lawyer familiar with the discussion told me, “Suffice it to say, if there was serious concern about revelation of sources and methods by the intelligence community you would have heard a lot of howling.”

Last fall, Holder selected the offices led by MacBride and Preet Bharara, the U.S. Attorney for the Southern District of New York, to prosecute the criminal case. Bharara, addressing the national-security concerns, said of Holder, “This is not a rogue Attorney General. These are reasoned, considered decisions made by people in America who have the greatest knowledge and concern about the revelation of these materials. And, with all due respect, they have greater knowledge than the critics.”

Holder told me that the “critical factor” in his choice of civilian prosecutors was that they could build a case independent of the Clean Team, and of the C.I.A.’s tainted confessions. His prosecutors, Holder said, had “constructed a case that uses materials and evidence that does not derive from the techniques that were controversial,” which would “maximize our chances for success.” It was a driving concern to Holder that the case not rest on torture. “It’s a statement about what this Administration is about,” he said. “It’s a statement about this Attorney General. We are not going to use the products of interrogation techniques that this President has banned.”

MacBride, like Holder, emphasizes the tactical advantages of the Administration’s approach. “There are gigantic challenges to attempting to cleanse concededly coerced statements,” he said. In fact, as Holder was making his decision the federal court in Washington was weighing another case involving the admissibility of statements made freely, after a prisoner had been tortured. In a decision that signalled trouble for the viability of Clean Team-type , prosecutions, U.S. District Court Judge Gladys Kessler ruled that the government must release another Guantánamo prisoner, Farhi Bin Mohammed, even though F.B.I. agents had elicited incriminating evidence against him from a fellow-detainee, Binyam Mohamed, without coercion. Her reason was that interrogators in Morocco had, among other abuses, cut Binyam Mohamed’s penis with a scalpel. After such mistreatment, Kessler found, it was impossible to regard later statements as free of taint.*

In Holder’s view, avoiding the Clean Team’s work was also smart in terms of winning the “hearts and minds” of the Islamic world. “Values matter in this fight,” he said. “We need to give those who might follow these mad men a good sense of what America is, and what America can be. We are militarily strong, but we are morally stronger.”

At the White House, Emanuel, who is not a lawyer, opposed Holder’s position on the 9/11 cases. He argued that the Administration needed the support of key Republicans to help close Guantánamo, and that a fight over Khalid Sheikh Mohammed could alienate them. “There was a lot of drama,” the informed source said. Emanuel was particularly concerned with placating Lindsey Graham, the Republican senator from South Carolina, who was a leading proponent of military commissions, and who had helped Obama on other issues, such as the confirmation of Supreme Court Justice Sonia Sotomayor. “Rahm felt very, very strongly that it was a mistake to prosecute the 9/11 people in the federal courts, and that it was picking an unnecessary fight with the military-commission people,” the informed source said. “Rahm had a good relationship with Graham, and believed Graham when he said that if you don’t prosecute these people in military commissions I won’t support the closing of Guantánamo. . . . Rahm said, ‘If we don’t have Graham, we can’t close Guantánamo, and it’s on Eric!’ ”

At Emanuel’s urging, Holder spoke with Graham several times. But they could not reach an agreement. Graham told me, “It was a nonstarter for me. There’s a place for the courts, but not for the mastermind of 9/11.” He said, “On balance, I think it would be better to close Guantánamo, but it would be better to keep it open than to give these guys civilian trials.” Graham, who served as a judge advocate general in the military reserves, vowed that he would do all he could as a legislator to stop the trials. “The President’s advisers have served him poorly here,” he said. “I like Eric, but at the end of the day Eric made the decision.” Last week, Graham introduced a bill in the Senate to cut off funding for criminal trials related to 9/11.

Behind Graham’s opposition was an insistence that Obama not treat military commissions as second-class justice. Given the commissions’ erratic track record, the argument strikes many legal observers as dubious. But once Obama had agreed to keep the commissions going he forfeited the option of openly criticizing them. David Cole, a law professor at Georgetown University, said, “They can’t say military commissions are less legitimate, because they’re still using them. But if they tried K.S.M. in a military commission they’d lose any chance of having a conviction seen as legitimate by the rest of the world.”

Once Holder had settled on taking the 9/11 cases to court, the remaining question was where. A confidential security study by the U.S. Marshals Service tipped the decision toward Manhattan. The marshals concluded that the courthouse on Foley Square was by far the safest option; it has underground tunnels through which defendants can be transported from the adjacent Metropolitan Correctional Center. In addition, Holder was mindful of a federal death-penalty statute that calls for capital-murder trials to be held in a state that is connected to the crime. The choice also may have had special significance for Holder because he was born and raised in New York City—in Queens, near LaGuardia Airport. His mother still lives in the city, and his brother William, a retired Port Authority police officer, lost several friends and colleagues on 9/11. In announcing his decision, Holder stressed that, “after eight years of delay, those allegedly responsible for the attacks of September 11th will finally face justice. They will be brought to New York—to New York—to answer for their alleged crimes in a courthouse just blocks away from where the Twin Towers once stood.”

Hours before he went public, Holder spoke with several New York officials, including Bloomberg, Schumer, and Governor David Paterson, all of whom pledged their support. Bharara, the U.S. Attorney, informed Commissioner Kelly. Holder then called Obama to relay his decision. Everything seemed in place. After Holder announced the plan, Bloomberg said, “It is fitting that 9/11 suspects face justice near the World Trade Center site, where so many New Yorkers were murdered.”

But the Obama Administration’s political preparations for a controversial trial were less thorough than those made by previous Administrations. In 1995, Justice Department officials spent months laying the groundwork for trying the bomber Timothy McVeigh in Oklahoma City. Detailed cost estimates were made, and there was extensive outreach to local officials, victims’ families, and security personnel. (Ultimately, a judge ordered the trial moved to Colorado.) By comparison, local officials in New York have said that they were only glancingly consulted. And, when the Foley Square protest made clear that some families of 9/11 victims were upset by the idea of a civilian trial, the White House barely reacted, and did not rally 9/11 families who favor a trial.

Now that Bloomberg, Kelly, and Schumer have withdrawn their support, the Justice Department is in retreat, and Holder is scrambling to find a venue for “the trial of the century.” Kate Martin, the Center for National Security Studies director, warns, “We can’t have a situation where political pressure forces the federal government to forgo criminal prosecution. That would mean the system is fundamentally broken.” Bill Martel, of Tufts, said, “When public fear coalesces, it generates forces that are almost uncontrollable by the political leadership.”

Late last month, at home, in Northwest Washington, Holder addressed those who have suggested that he and Obama are too weak to take on terrorism. “This macho bravado—that’s the kind of thing that leads you into wars that should not be fought, that history is not kind to,” he said. “The quest for justice, despite what your contemporaries might think, that’s toughness. The ability to subject yourself to the kind of criticism I’m getting now, for something I think is right? That’s tough.” He paused, and added, “This is something that can get a rise out of me, the notion that somehow Eric Holder and Barack Obama, this Administration, is not tough. We have the welfare of the American people in our minds all the time. We’ll fight our enemies, and we’ll do that which is necessary, and we won’t turn our backs on the values and traditions that have made this country great. That is what is tough.” ♦

*Corrections, February 5, 2010: The original text stated that Binyam Mohamed had been tortured during an interrogation related to his own case, and that he, not Farhi Bin Mohammed, was released by Judge Kessler.

**Ogden announced his decision to resign last December; he did not resign last December, as originally stated.