On Monday, October 3, a frightened and vulnerable Judith Miller walked into *The New York Times'*s cluttered Manhattan newsroom. It was the first time in three months she'd been inside the only professional home she'd known since 1977. Four days earlier, Miller had been released from Virginia's Alexandria Detention Center, where she'd been incarcerated after refusing to testify in front of a federal grand jury investigating whether government officials had leaked the identity of undercover C.I.A. operative Valerie Plame Wilson. After 85 days in jail, Miller, aware that she could end up spending more than another year behind bars, had negotiated a deal that allowed her to testify. ("I don't want to spend my life in here," she'd told a friend while in Virginia.) Miller's imprisonment, and her release, had made her a central figure in a scandal that was threatening to envelop the White House, as special prosecutor Patrick Fitzgerald homed in on Bush-administration officials who now seemed destined to be indicted for their role in the case.

Miller was not the first writer, or the first Times reporter, to have been jailed for refusing to share confidential information with government officials. In 1978, the *Times'*s Myron Farber was imprisoned for 40 days for his refusal to hand over notes in a murder trial. As recently as 2001, Vanessa Leggett, a former private investigator who was working on a book about the killing of a Houston socialite, stayed in jail for 168 days rather than turn over her notes to prosecutors. Unlike Miller, both Farber and Leggett were released from jail without having to reveal any confidential information.

In Farber's case, as in Miller's, the Times had waged a passionate crusade on its reporter's behalf, and for seemingly good reason: there is no greater sacrifice, and no greater test of the journalist's code of ethics, than going to jail for refusing to name a confidential source. Without reporters' ability to promise confidentiality to those willing to share information that their bosses—or the government—might not want published, journalism as we know it would grind to a halt. During Miller's imprisonment, the paper's editorial page—run by Times publisher Arthur Sulzberger Jr. and editorial-page editor Gail Collins—published piece after piece championing Miller as a highly principled American hero. "We stand with Ms. Miller and thank her for taking on that fight for the rest of us," read one typically crusading column.

In the *Times'*s third-floor newsroom, Miller was not given a hero's welcome. (She had been so wary of the reception she might receive that she'd asked a friend to escort her into the building.) The more than 100 reporters and editors who had gathered in the center of the room—traditionally the site of Pulitzer Prize celebrations—greeted Miller with tepid applause. Miller, always slim, had lost quite a bit of weight during her confinement and looked pale and frail under her trademark pageboy.

Bill Keller, the paper's executive editor, acknowledged the tension in the room. "I know that you and our readers still have a lot of questions about how this drama unfolded," Keller told the assembled staff in a drawl that was at once folksy and patrician. "Now that she's free, we intend to answer those questions to the best of our ability in a thoroughly reported piece in the pages of The New York Times, and soon. We owe it to our readers, and we owe it to you, our staff." Keller was right. Times employees, along with the rest of the country, were wondering what, exactly, Miller's relationship had been with I. Lewis "Scooter" Libby, the source she had seemingly gone to jail to protect, and whether she was the right reporter on whose behalf to wage a campaign. Most pressingly, they wondered what, exactly, had changed to allow Miller to testify after both Miller and the Times had so passionately and persistently argued that no amount of jail time would compel her to reveal her sources.

Keller had already set some of the newsroom's most trusted journalists on the case. Earlier that day, reporters David Barstow and Adam Liptak and editor Jon Landman had gone out to lunch at Virgil's, a Times Square barbecue joint that Landman is especially fond of, to discuss putting together a report on Miller and her saga. Barstow, a highly respected reporter at the paper, and Liptak, a former Times in-house counsel and now the paper's national legal correspondent, had worked together on a similar project two and a half years earlier, the 14,000-word dissection of the Jayson Blair fiasco. Landman, the paper's deputy managing editor, would oversee and edit the story. Over lunch, Barstow, who had been asked by Keller the previous Friday to work on the project, said he was unsure if it would be appropriate for him to join the team. He'd sat next to Miller in the paper's investigative unit for several years and was close to the controversial correspondent. (Indeed, Miller herself had asked Barstow to work on the story.) Throughout lunch, Landman and Liptak tried to convince Barstow he could be an asset to the team. "I wanted him on," says Liptak. "I wanted him on because I just think he's so good. But [Barstow] was right."

Back in the newsroom, Susan Edgerley, the paper's metropolitan editor, asked reporter Janny Scott if she could speak with her. "She led me all the way across the newsroom into her office," Scott, known as one of the paper's better writers, remembers. "And she had a look on her face like … I don't know. I was worried I had really screwed up on something. I mean, she's very jolly normally." Once inside her office, Edgerley closed the door and asked Scott to join the team.

Barstow, meanwhile, was wrestling with the decision he had to make. Eventually, he asked Don Van Natta for his advice. Van Natta, another member of the paper's investigative team, had recently returned to New York from a posting in London. Van Natta had worked with Miller before—the two had even shared a byline on a story in a 2001 series that eventually won a Pulitzer. "I knew he had a very close relationship with Judy," Van Natta says of Barstow. "And I said to him immediately, 'Absolutely not. You can't work on this.'"

Van Natta himself, however, had no such conflicts. That night, he met his old friend the Washington, D.C.–based Times columnist Maureen Dowd at the Royalton Hotel for dinner. A group of Dowd's closest allies from the paper were there, including TV reporter Bill Carter, book critic Michiko Kakutani, and managing editor Jill Abramson. At one point, Abramson took Van Natta, with whom she is very close, aside. "Don, I need you for something," Abramson said. "I need you to work on the Judy Miller story."

On that unseasonably warm day in early October, writing the *Times'*s own account of the Miller tale must have seemed like an unenviable assignment, but one that could be completed without too much hassle. Keller had already implicitly promised that the team would get full access to all areas of the newspaper. Miller herself had said just that afternoon that she would cooperate with the paper's reporters, before hastily adding that she might also write up her own account in a book.

But the process of shepherding the story into print would be anything but smooth. It would be two full weeks and several blown deadlines before the *Times'*s account of Miller's story—and Miller's own dispatch describing her grand-jury testimony—made it into the pages of The New York Times. By then there was no longer any illusion that Miller was being greeted with open arms or that the circumstances of her jailing and release were anything but deeply troublesome for the Times. The Times reporters working on the story found that the editorial board and many of the paper's top executives either refused to speak with them or were prohibited from doing so. Sulzberger himself had explicitly barred at least one executive from speaking about the case. (According to people who have seen a transcript of the interview, when the reporters pressed Sulzberger on why he had refused to allow Russ Lewis, the former president and chief executive officer of the Times Company, to speak to them, Sulzberger replied with a laugh and this quip: "Because I don't know what the fuck he's going to tell you." Lewis, according to several newsroom sources, had been instrumental in crafting the paper's initial response in the Miller case. When asked to comment for this article, Sulzberger wrote in an e-mail, "Thanks, but I think I'll pass.") Miller herself refused at various times to talk to either Adam Liptak or Janny Scott and complained about Don Van Natta's reportorial techniques.

Now, several months after Miller's release, few of the complicated questions raised by her case have been answered to anyone's satisfaction. Should journalists' conversations with their sources be given protected status, similar to those between doctors and patients or attorneys and clients? Did Judy Miller's ultimate decision to testify represent a victory for journalists, or did it inexorably damage the future ability of journalists to withstand the pressure of prosecutors?

Pressing as these questions are, within the Times itself they are taking a backseat to concerns about the paper's direction and the leadership of Sulzberger, who, in addition to being publisher, serves as the Times Company's chairman. Just two years earlier, the *Times'*s reputation had survived—barely, some would say—one of its worst public humiliations ever, when Jayson Blair hoodwinked the paper with a series of fabrications that led to the dismissal of its two top editors and a shaken public trust. In the years since then, the business side of the paper seemed to be floundering. Since June 2002 the *Times'*s publicly traded stock has been on a steady decline, from a high of $52.79 to a November 2005 low of $27.23. Even before Miller went to jail, employees on the editorial and business sides alike were questioning many of the Times Company's business decisions, including its aggressive staffing of the Paris-based International Herald Tribune; its $410 million purchase of About.com, a collection of Internet guides; and its much delayed building of a new headquarters (all of which were occurring in the period before the Times announced a round of layoffs in May). With the Judith Miller imbroglio—which, according to the Times, cost the paper millions of dollars in legal bills alone—added to the mix, concern about Sulzberger, after bubbling just below the surface for years, began to boil over. What, exactly, was going on? And what did it mean for the future of the paper itself?

Bill Keller's ascension into the *Times'*s executive editor's drab third-floor offices on July 30, 2003, was less than typical. Keller rose to what is arguably the most esteemed (and important) job in American journalism thanks to the very public and very messy meltdown of the newspaper under his predecessor and rival, Howell Raines.

In May 2003, less than two years into Raines's tenure, Jayson Blair had exploded like a suicide bomber in the *Times'*s newsroom. Before Raines or Sulzberger realized what was happening, the Times had erupted into an astonishing six-week period of open revolt, one which ended only with Sulzberger's firing of Raines and his installation of Keller. It was Raines who lost his job, but within the Times the most persistent questions were being asked about Sulzberger. Why was it that, despite more than a year's worth of increasingly anxious warnings, Sulzberger had seemingly remained oblivious to the damage the blindingly imperious Raines was inflicting on the newsroom? Through the course of the crisis, Sulzberger—who'd long been plagued by questions about his maturity and judgment—was mocked for what many of his staff saw as his glibness and insouciance.

Upon taking over, Keller worked to soothe an institution that was suffering from what many staffers described as a kind of collective post-traumatic-stress disorder. Reporters weren't speaking with editors, factions had developed within the paper, and a pervasive sense of unease and distrust marked many interactions.

After surveying the landscape, Keller recognized that dealing with Judith Miller would be one of his first challenges. Miller had been controversial for as long as she'd been wielding a notebook. She was relentless, indefatigable, ultra-competitive, and extremely well connected. (She dated Steve Rattner, one of Sulzberger's best friends when the three of them worked at the *Times'*s Washington bureau, and had even, for a time, shared a vacation home with Sulzberger.) She had a reputation for sleeping with her sources (in the 1980s, she both lived with then congressman Les Aspin and quoted him in her dispatches); for bigfooting her way onto other people's beats; for raining down torrents of abuse on clerks, travel agents, and drivers; and for cutting down her colleagues. She had her defenders on staff, those editors and reporters who marveled at her determined pursuit of a story, her deep sourcing, her tirelessness, and her work ethic. "She's incredibly focused," says a colleague. "I see a lot of people who come in and spend most of their day playing internal politics and reading [the journalism blog] Romenesko and gossiping, and I look at her and I see someone who is single-mindedly focused on her work, sometimes to her own detriment. She spent very little time making friendships."

Miller had been covering threats to national security—one of the biggest, most important beats on the paper—since before Raines's installation, in September 2001. She was working under investigative editor Stephen Engelberg, and was, according to Times staffers and editors familiar with her work at the time, supervised very closely. For a while it seemed as if the Times had finally hit upon a formula that made Miller's sharp elbows worth the trouble. She was recognized as one of the lead journalists on a project that had, in 2001, dissected the "global terrorism network and the threats it posed" and won the Times one of its seven 2002 Pulitzers. Her work on the Pulitzer project made her even more appealing to Raines, an editor with a taste for flashy exposés and prizewinning packages.

Soon after she won the Pulitzer, however, Miller's safety net began to dissolve. First, Engelberg, increasingly frustrated by what he saw as Howell Raines's desire to ram sensational stories into the paper, quit. It was during this time, according to a Times story, that Miller referred to herself as "Miss Run Amok" because, as she said, she could "do whatever I want." Times editors began to complain that Raines refused to allow substantial editing of Miller's work. The result was a series of credulous stories about weapons of mass destruction in Iraq that helped, in the eyes of many, to justify the administration's spin on the war.

Over time, the contempt and frustration directed toward Miller began to indicate a loss of perspective. For example, although Miller shared her byline with Michael Gordon in the now infamous September 8, 2002, front-page dispatch about Saddam Hussein's attempted purchase of aluminum tubes thought to be intended for use in centrifuges to enrich uranium, it was Miller who was usually blamed for what some considered the piece's evidence of gullibility, or even willful shilling on behalf of the administration. In fact, it had been Gordon who brought in the aluminum-tubes aspect of that story. (Gordon eventually wrote several corrective follow-ups on the issue.)

By the spring of 2003, when it became clear to most of the country that it was unlikely there were any W.M.D. to be found in Iraq, journalists around the country began writing increasingly critical reports on the government's claims. But the Times didn't reverse course, at least not right away. Instead of looking for ways to shore up the paper's W.M.D. coverage, Raines was struggling desperately to save both his job and his reputation.

This was the situation Bill Keller faced as he took over. He knew that the paper's pre-war reporting and Miller's embedment with a team of soldiers sent to hunt for W.M.D. in Iraq would only draw more criticism as time went on. (Keller declined to comment for this article.) He also believed that he had to try to mop up the blood on the floor before he attempted to do any more housecleaning. He decided to put off publicly examining the *Times'*s weapons reporting for as long as he could; in the meantime, he'd assign some of the best journalists he had to re-examine the W.M.D. issue. That way, the paper could solve the problem with good reporting. Finally, he told Miller that she was not allowed to cover W.M.D. or national security. This, he thought, would at least minimize the damage Miller could do going forward.

He was wrong. While Times editors repeatedly batted down Miller's story ideas, Miller continued to report on national security, continued to meet with her sources in the White House and in the intelligence community. (Miller has said that she was not permitted to report on weapons issues and that she was assigned stories related to national security.) And now, two years later, the Judith Miller problem had grown bigger than ever.

By Tuesday, October 4, David Barstow had told Jon Landman that, because of his friendship with Miller, he'd be unable to work on the team. That left Adam Liptak, Janny Scott, and Don Van Natta. Landman was hoping to get at least a provisional story explaining Miller's role in the leak case into the paper by the weekend, for the Sunday, October 9, edition. He decided he needed at least one more reporter, and he asked another of the paper's editors to approach Clifford Levy.

Levy is what newshounds call a "doc" guy—he has a remarkable ability to pore through thousands of pages of complicated documents. Initially, the work he was assigned to on the Miller project was relatively contained. "[Landman] wanted me to go through all the editorials that the paper had written on the Miller case and write a section on what the paper's editorial views had been over those many months," Levy says.

By Wednesday, October 5, it appeared Levy would be needed for more than simply that—he'd help write the story, and would also help sort through the incredible amounts of information coming in. ("As soon as it became clear we were doing this, everyone wanted to call in with their own Judy horror story," one of the reporters said.) Liptak, the former Times lawyer, would focus on the First Amendment and legal issues raised in the case. Scott would report on the activity inside the Times building—on Sulzberger, for example, and on the paper's editorial board. And Van Natta would concentrate on Miller and her Washington-based lawyer, Bob Bennett, in addition to helping Liptak with legal issues. (Van Natta had been one of the *Times'*s lead reporters on the Monica Lewinsky case, in which Bennett defended President Clinton.)

Miller, it soon became clear, was not going to be an easy source to deal with. She initially refused to speak with Liptak because, she said, his story about her release from jail implied that she hadn't gotten a better deal from the prosecutor than the one that was available to her before she was imprisoned. She refused to speak with Scott because, she told friends, Scott had not bothered to write to her when she was in jail. (She also told people that she knew Scott was "judging" her.) At various points she wouldn't speak with Van Natta either. On Tuesday afternoon, Van Natta approached Miller in the *Times'*s newsroom. Miller immediately gave Van Natta a hug. "I'm so glad you're involved in this," Miller said. "Well, I'd really like to talk to you, now, if you have time," Van Natta replied. "I can't do it now," Miller answered. "I'm running off to go meet with Barbara Walters."

"That was pretty amazing to me. I'm a colleague of hers, I'm trying to get an interview, and she doesn't have time for that, but she has time for Barbara Walters. And that night she did another one with Lou Dobbs." The next day, Van Natta ran into Miller again, in Bennett's Washington office; at that point, Miller told Van Natta she couldn't speak with him because Libby had given her permission to talk only to the grand jury. That's odd, Van Natta told her. On Monday in the newsroom, she had told the whole world Libby was her source.

"We knew it was not going to be easy dealing with Judy," Van Natta said. "At that point her stance was basically not to cooperate with us at all, and the things she was saying were just so preposterous. Sometime during that week I began to think to myself, I get it. She's saving it all for a book." (Miller did eventually agree to speak with the reporters on the record and to this day insists she was fully cooperative.)

By Friday night, October 7, Landman and his crew were at their wit's end. They stayed up most of the night trying to write a piece that would at least explain Miller's role in the leak case, but without any of the details of her grand-jury testimony, they couldn't come up with much.

"There was no logical reason why she couldn't tell us her testimony," Liptak says. "To hear her tell it, she was afraid she may be called as a witness at Libby's trial. I guess the thinking is that she's given one version under oath, and if she says or writes something that's at odds with that, she's potentially a perjury target. The answer to that dilemma, of course, is to always be consistent and truthful." Despite having little to work with, by early Saturday morning, the team had cobbled together a story they hoped to get into Sunday's edition.

"I printed it out at three in the morning and I read it in the cab home," says Liptak. "And I just said, 'This thing sucks and I don't want my name on it.' It didn't begin to answer any of the larger questions about what was really going on here. If this was the answer to the promise we'd made to our readers about coming clean, it was just inadequate."

Early on Saturday morning, Landman, Levy, Liptak, and Van Natta reconvened in Landman's office. They all agreed the piece couldn't run. Miller was scheduled to testify once again in front of the grand jury in the coming week, and maybe, the team thought, she'd be more cooperative after that.

Meanwhile, the Times newsroom began to percolate with rumors. Had Sulzberger personally killed the story? Was the piece ever going to run? "There was this enormous pressure, both from within the paper and from the outside world, to get this thing in," says one of the reporters. "And then when it didn't appear, I got these e-mails saying, 'Just tell me the truth. Has it been killed?' There were so many conspiracies, about Arthur protecting her, or whatever. It was insane."

The pressure only increased over the next week. Miller kept avoiding having on-the-record conversations with Van Natta; at one point, she complained to Keller about Van Natta's line of questioning, and Van Natta felt she was trying to have him removed from the story. (Miller did something similar in my case. After I approached her for this story, she complained to the editor of this magazine and raised questions about my allegiances. She also wrote to me in an e-mail, "Seth, I read what you wrote about me in your book. You never bothered to check any of your alleged facts about me. I have absolutely no intention of talking to you." Three weeks later, after the story had been written and edited, she sent another e-mail that read, "When you are finished with your research, and want my input before you write, send me a list of questions." I sent Miller questions on two occasions, to which she never replied. Outside of noting that Miller's pre-war W.M.D. reporting was faulty—which Miller herself now acknowledges—there are barely any mentions of Miller in Hard News, my book about Howell Raines and the Times. What's more, while writing it, I tried to reach her numerous times for comment. She never responded.)

Miller was also delaying handing in a first-person account of her grand-jury testimony. Part of the problem was that her lawyers were dead set against her writing anything that characterized her testimony. David Barstow, meanwhile, was trying to convince his colleague that, having gone to jail to protect the public's right to know, and now having testified, she owed it to her readers to give an account of her testimony in the pages of the Times. That week, both Keller and Miller asked Barstow if he would help shepherd Miller's story into the paper. On Wednesday night, as Miller returned from Washington after her second time testifying in front of the grand jury, Barstow met her at Penn Station.

Miller was exhausted. She eventually rejected her lawyers' advice, and worked with Barstow throughout Thursday and Friday to get her story into the paper. Even so, the two stories weren't completed until the deadline for the *Times'*s bulldog edition (a Sunday paper that's released late on Saturday) had already passed.

When Judy Miller was subpoenaed in August 2004, her decision not to testify was viewed through a charged, politicized prism. People both inside and outside the Times were arguing that Miller, instead of refusing on principle to name a source for a story she had never even written, was engaged in something far more nefarious. She was protecting her allies within the administration. Or maybe she was even the initial source of the leaked information. At the very least, the thinking went, she was trying to salvage a reputation sullied by several years' worth of criticism over her war reporting.

But at the highest level of the Times, Miller was not being viewed with any skepticism or wariness; instead she was seen as a possible martyr. Sulzberger had struggled to prove he was the right man for the job since the day he took over from his father, Arthur "Punch" Sulzberger, in 1992. More than three decades before the Miller saga, in 1971, Punch Sulzberger had fought one of the defining battles of his career, when the Times argued before the Supreme Court for the right to publish the Pentagon Papers, a secret history of the Vietnam War leaked to the paper by Daniel Ellsberg. Now it seemed that Arthur Sulzberger Jr. was looking for his own Pentagon Papers case.

"There was a perfect-storm aspect to all of this," says a Times journalist intimately familiar with the details of the Miller case. "Post-Howell, Arthur and Judy were both looking at resurrecting their reputations. And Arthur was so oblivious he didn't care about the repercussions." A business-side employee is even more frank. "Arthur's very well intentioned. But there's something approaching panic about the way he deals with things. There have been a lot of very messy problems in not a lot of years. We could all see this was not the right fight to pick. But he was so determined to push ahead."

This past summer, when Judith Miller was jailed, the *Times'*s editorial page immediately took up her cause. Repeatedly, it bragged of Miller's steely resolve. "It should be clear after 41 days in a Virginia jail that Ms. Miller is not going to change her mind," an August 15 editorial read. "If she is not willing to testify after 41 days, then she is not willing to testify." For his part, Sulzberger said that he wouldn't go to a single Bar Mitzvah without talking of Miller's plight. As editorial after editorial appeared in print, people in the *Times'*s newsroom began to get more and more anxious. Are we sure, many asked, this is the right fight for us? (Gail Collins, the *Times'*s editorial-page editor, would not talk to the reporting team about the paper's editorial policy. When asked to comment for this article, Collins wrote to me in an e-mail, "We actually don't talk about the editorials in general. The theory is that they should speak for themselves.")

The collective anxiety surrounding the *Times'*s support of Miller seemed prescient after Miller struck the deal that she said allowed her to testify. When the leak case began, the F.B.I. circulated blanket waivers to White House employees that would give reporters permission to break any promises of confidentiality. Initially, Miller said she felt that the blanket waivers were, by their nature, coercive, and that communications she had had with her source indicated to her that he didn't really want her to break her promise of anonymity. George Freeman, the *Times'*s in-house counsel, and Floyd Abrams, the First Amendment lawyer who had argued for the *Times'*s right to publish the Pentagon Papers, in 1971, agreed.

Once he joined the case, Bob Bennett increasingly agitated to strike a deal. ("I don't want to represent a principle," Bennett told Miller upon taking her case. "I want to represent Judy Miller.") As Miller spent more and more time in jail, Bennett began to argue that Fitzgerald would likely convene a new grand jury after October 28, when the term of the initial one ended. That meant that Miller, instead of serving just under four months in jail, could have ended up spending almost two years behind bars. At the same time, Miller's husband, New York Review of Books founder Jason Epstein, was urging his wife to give up the fight.

Other lawyers involved felt Bennett's efforts to strike a deal with a source once Miller was already in jail would have potentially disastrous results. "I thought then Fitzgerald would not move to keep her there longer," said one lawyer involved in the case. "And I thought it would be horribly damaging to [Miller's] reputation if she left after cutting what seemed like a very similar deal to what she had been offered at the outset." Bennett, who didn't respond to requests for comment, prevailed, and eventually reached out to Libby and had him clarify what he had communicated through his lawyer a year earlier: that Miller was free to testify. As part of the deal, Fitzgerald also promised Miller that the grand jury would limit its questions to Scooter Libby and the Wilson case.

"When Judy took that deal, I was so crushed," said one colleague. "Her argument that waivers are by definition coercive was the right one. If anything, it's more coercive to go back to a source when you're in jail and say, 'Are you sure you really want me to rot away in here protecting you?'"

Even Myron Farber, the Times reporter who had been jailed almost three decades earlier, expressed dismay. "I just can't imagine doing it," he told Editor & Publisher. "I am just against the notion of waivers. When I was in jail, the thought of accepting one never crossed my mind."

On Sunday, October 16, more than two weeks after her release, the Times published its 6,000-word dispatch on Miller's case, accompanied by the Barstow-guided account of Miller's grand-jury testimony. The two stories highlighted the degree to which Miller was seen as a renegade reporter, and included details of her unusual sourcing arrangements, murky security clearances, and Miller's apparent misleading of her editors.

Before the Times report was even published, Bill Keller, perhaps remembering the disastrous "town hall" meeting that had been convened in the wake of the *Times'*s report on the Jayson Blair affair, decamped for a previously scheduled tour through Times bureaus in the Far East. While he was away, newsroom frustrations over Miller mounted. Finally, Keller decided to send out a memo which arrived in in-boxes on Friday, October 21. "I wish we had dealt with the controversy over our coverage of WMD as soon as I became executive editor," Keller wrote from Asia. He also addressed the Miller saga. "In this case I missed what should have been significant alarm bells. Until Fitzgerald came after her, I didn't know that Judy had been one of the reporters on the receiving end of the anti-Wilson whisper campaign. I should have wondered why I was learning this from the special counsel, a year after the fact.… If I had known the details of Judy's entanglement with Libby, I'd have been more careful in how the paper articulated its defense, and perhaps more willing than I had been to support efforts aimed at exploring compromises."

The next day, Times columnist Maureen Dowd entered the fray, calling Miller a "woman of mass destruction" who gravitated toward powerful men. Dowd accused Miller of stenography, of lacking credibility, of being outrageous and frantic. If Miller were to return to the Times, Dowd wrote, "the institution most in danger would be the newspaper in your hands." Finally, on Sunday, October 23, Times public editor Byron Calame wrote a harshly critical column about Miller in which he concluded, "The problems facing her inside and outside the newsroom will make it difficult for her to return to the paper as a reporter."

The Times, suddenly, seemed to be engaged in a lynching of a reporter it had just spent months defending. Keller was criticized for using the loaded word "entanglement" when "conversations" would have sufficed. Gadflies like the New York Post and Don Imus delighted in amping up the conflict between Dowd and Miller. ("Punchin' Judy: A Catfight Breaks Out at Paper of Wreckage," screamed the New York Post the day after Dowd's column ran.) Sulzberger, meanwhile, seemed to scramble to make his voice heard. "Bill spoke for the newsroom but I concur with his position," he said in a Wall Street Journal article published Monday, October 24. "In that regard, some of Bill's 'culpas' were my 'culpas' too."

Miller, to the surprise of no one who knew her, dug in her heels and prepared for a fight. Instead of taking several months off, as she initially indicated she'd do, she began to make noises about returning to the Times immediately. One source says she called friends and advisers to tell them that had Keller or Sulzberger ever asked to see her notes, she would have shared them without any problem. She demanded she be given space to write an op-ed column refuting the charges against her. She had all-day meetings with lawyers and private conferences with Sulzberger.

Meanwhile, she continued to be defiantly visible in Manhattan and Sag Harbor, on Long Island, where she and Epstein live. Miller sightings began to take on the currency of spotting Leo and Giselle canoodling with their new partners. One day she was seen walking through Times Square, the *Post'*s "Page Six" reported. On another, she was seen having breakfast at Balthazar with columnist Andrea Peyser, said the gossip Web site Gawker. She was out "giggling at the bar" at a party thrown by Knopf editor in chief Sonny Mehta and Viacom executive Tom Freston and his wife, Kathy, according to Women's Wear Daily. The New York Observer ran thousands of words on her social engagements, describing dinner with financier Felix Rohatyn and Council on Foreign Relations chairman Pete Peterson, coffee with Simon & Schuster editor Alice Mayhew, and support from the likes of novelist E. L. Doctorow and Daily News owner Mort Zuckerman.

Finally, on Wednesday, November 9, Miller and the Times severed their ties. In another staffwide e-mail, Keller announced that Miller had resigned from the paper, effective immediately. At the end of his memo, he included a personal letter he'd written to Miller in which he apologized for his use of the word "entanglement"—it was not meant, Keller wrote, "to suggest an improper relationship." Keller also acknowledged that there remained some disagreement as to whether Miller had ever misled her editors at the paper. The next day, the Times printed Miller's 735-word letter to the editor, in which she defended her reporting, hyped her Web site, and wrote that she was resigning because, "over the last few months, I have become the news, something a New York Times reporter never wants to be."

Miller, however, certainly isn't behaving like someone who doesn't want to be making news. Her Web site (which prominently features a demure headshot on every single page) contains self-justifying posts and cherry-picked, laudatory articles; her sundry responses to various Times critics take up more than 3,000 words on their own. The day after resigning from the Times, she spent an hour on Larry King's CNN show, throwing darts at Dowd ("I just want to talk about the serious attacks and criticisms," Miller said when first asked about her former colleague) and hinting that she might end up as a columnist one day.

But it'll be harder than that for Miller to turn the page. One of the biggest legacies of this year's saga will not be the interpersonal soap operas caused by Miller's spectacular flameout, but the fact that prosecutors have been shown, once and for all, that jail does work as a way to break reporters' wills. After all, even the indomitable Judy Miller cracked. Miller, undoubtedly realizing that this point will be contentious for years to come, continues to insist that the deal she got with Libby was substantially different than what she was offered before she went to jail. "I wanted a personal, written letter from Scooter Libby saying, Judy, I want you to testify. And I wanted the right to question him about whether or not that letter was really voluntary," Miller told King. But Libby wrote in his letter that he was only re-stating what he had said a year earlier—that he had voluntarily waived his rights to confidentiality. And the conversation Miller eventually had with Libby was not an intimate discussion between a reporter and her source but a jailhouse conference call with several lawyers in attendance. As we now know, Miller's testimony was extremely damaging to Libby. Denying that he was the source of Wilson's identity, Libby told Fitzgerald he had actually heard that information from reporters. Miller was the final nail in Libby's coffin, and on October 28 he was indicted for obstruction of justice, perjury, and making false statements. (As ABC News's Jake Tapper pointed out, the Times, by openly questioning Miller's credibility in print, has handed Libby's defense a potential gold mine.)

It will likely prove just as difficult for The New York Times to move forward. The *Times'*s top editors seem to have escaped most of the criticism that drowned Howell Raines in 2003 (although observers in the newsroom have noted that it was managing editor Jill Abramson, in her role as Washington-bureau chief, who was responsible for editing some of Miller's W.M.D. dispatches). Sulzberger has not been so lucky. For the second time in less than three years, he's being accused by his employees of being dangerously out of touch. Why, with a newsroom already so divided about Miller's behavior, did he need to wage such a public campaign on her behalf? "I feel it's as inevitable that Arthur's going to go as I felt it was that Howell was going to go," says an editor at the paper. That's probably an overstatement. Sulzberger's position can be threatened only by members of his family, who control the Times Company's Class B voting stock. But since Miller got out of jail, there's a mantra that's been repeated in the *Times'*s newsroom: If Judy is the new Jayson, then Arthur is the new Howell.

The same night Miller chatted with Larry King, Sulzberger appeared on Charlie Rose's PBS show. The hour-long interview was seen as something between a wash and a disaster by more than a dozen reporters, editors, and business-side employees I spoke with. Outside critics were even harsher. "Sulzberger's jabber," *Slate'*s Jack Shafer wrote of the performance, "differs not one whit from the standard bullshit—'Move along folks, there's nothing here to see'—issued by every politician and corporate leader who finds himself trapped in the media's crosshairs. When a news subject relies on such transparent talking points as 'it's time to move on,' reporters know the story is only beginning."

"We all know The New York Times is what it is today because it's a family-owned operation," said a journalist who has spent decades working at the Times. "But when these things keep happening, it makes a lot of people wonder what it's going to take for some real changes to happen in the way this place is run."

Seth Mnookin is a Vanity Fair contributing editor.