With Miller now incarcerated for 43 days and counting, interviews with nearly a dozen Times staffers reveal widespread concern for Miller’s welfare and support for the principle for which she is being jailed. “It is extremely upsetting to see a colleague in jail,” says Adam Nagourney, a Washington correspondent. Adds Eric Schmitt, another D.C. colleague, “Everyone remains quite concerned about what happened to her.” “I think most people have nothing but sympathy for Judy’s situation,” noted Craig Whitney, an assistant managing editor and 40-year Times veteran. “And outrage that she has to go to jail for a principle that we all believe in.” Indeed, both inside the Times and elsewhere in journalism, the paper is being praised for standing by its reporter as she defends a journalistic tenet most in the industry find sacred.

But numerous staffers also have told Salon that Miller’s legal saga has become a burden, and not just for the paper’s 12-person in-house legal team, which has been swamped by her case. Troubling many staffers is the dark cloud of unanswered questions about Miller’s reporting and role in the Plame affair. Some at the Times contend that Miller has drawn unwanted attention to the paper at a time when it is still healing after the Jayson Blair fiasco dealt a body blow to its credibility. “It is a big bet for the paper,” one reporter who requested anonymity said of the Times’ unyielding support for Miller. “The paper chose to make this into something to fight to the death. It may have possible negative consequences for the paper’s image when people are spending an enormous amount of time and energy on the credibility of the paper.” Although several Times staffers were willing to offer criticism of the paper, none would do so on the record for fear of retaliation.

The grumblings inside the Times have grown louder as more questions have been raised about the scope and nature of Miller’s role in “Plamegate.” Many of Miller’s colleagues are unclear about exactly whom or what Miller is protecting. In the face of limited information, some speculation has surfaced that Miller is only pretending to protect a source to divert attention from her past problems. No proof exists that the theory is true.

More prominently, a recent report that Miller met with I. Lewis “Scooter” Libby, Vice President Dick Cheney’s chief of staff, less than a week before Robert Novak outed former CIA agent Valerie Plame in a 2003 column, has added to the speculation over what role Miller may have played in the leak of Plame’s identity. The theory being peddled on the Huffington Post and elsewhere in the lefty blogosphere has Miller not on the receiving end of information from an administration leaker about Plame’s identity, but as the one disseminating information about Plame to administration officials. This is just a theory, of course, with no known evidence supporting it. But it’s fair to say that many Times staffers want Miller’s role in the Plame affair clarified, and some of her Times colleagues are downright angry about what is known, and unknown, about her involvement.

Although Miller never wrote a story about Plame, she is one of several journalists targeted by special prosecutor Patrick Fitzgerald in his investigation of who leaked the agent’s identity more than two years ago. Although Fitzgerald has subpoenaed and interviewed several reporters, Miller is the only one who has so far refused to disclose her sources, prompting a federal judge to sentence her to jail until either she gives up the source or the grand jury ends its work, likely sometime in October.

Some insiders claim the Miller case has sparked new questions from Times critics — and employees — about the paper’s credibility given Miller’s controversial past. Other staffers say the paper has not been very forthright with employees about exactly what Miller knows, what she had been working on when she learned of Plame’s identity, and how much editors know about her sources.

“The most common denominator is that there are a lot of unknowns about it,” says one Times reporter, who did not want to be identified. “Both what happened, what’s going to happen, and how the case will proceed. There are different levels of knowledge.” Another reporter adds, “There are a lot of unanswered questions about what the editors really know and the public should know.”

Some staffers say Miller’s reputation as a hard-driving news person who “has stepped on a lot of toes” makes it difficult for them to back her completely. Others point to her questionable reporting in recent years related to the buildup to the Iraq war, in which she wrongly reported the likelihood of weapons of mass destruction in Iraq. Such reporting prompted the Times to publish an unusual editor’s note last year admitting it had failed to adequately question such claims.

“She is obviously a very contentious person,” one co-worker, who requested anonymity, said. “There are people who have a question about the integrity of [her] reporting.” Another colleague called her WMD reporting “a dark chapter.” “I’m not sure there is a lot of sympathy or support,” a third fellow reporter said about Miller. Her baggage even prompted one journalism group, the American Society of Journalists and Authors, to rethink giving her an award in early August for her efforts. After an ASJA committee approved the award, an outcry from some ASJA members sparked a reversal at the board level.

But reports from within the Times about growing discontent about the Miller case and the paper’s handling of it are in sharp contrast to how executive editor Bill Keller sees the situation. Responding via e-mail to submitted questions from Salon, Keller disputed reports that the case had drawn a lot of internal dissent. “A lot of things that are ‘reportedly’ true about this case and the newsroom reaction are either flat wrong or grossly inflated,” he stated. “I think the prevailing sense in the newsroom — regardless of what feelings individual reporters have about Judy and her past work — is that they are glad the paper is standing up for her and defending the principle of reporters’ need to protect their sources.”

Other editors also contend that they have not heard internal discord. “If any member of the staff dissatisfied about our internal communication approached me, I would try to get some answers, within the limits of our necessary protection of sources, of course,” assistant managing editor Allan Siegal said in a statement. “But no staff member has expressed that frustration to me.” Whitney offered a similar view, saying, “I am unaware of any undercurrent of discontent.”

Keller said he understood the staff concerns, but remains somewhat limited in what he can tell them due to the investigation and the involvement of a confidential source. “Believe me, I would like nothing better than to tell our staff whatever I know about this case. But we have a colleague who has been in jail for more than a month, and I’d need an awfully compelling reason to divulge information that could in any way complicate her situation further,” Keller wrote. “I’ve talked about this case a lot — in public, in interviews with various news organizations, and more privately with members of the staff — but I have a responsibility to be cautious.”

As for the paper’s image, Keller remains unconcerned, saying the journalistic principle involved is more important. “It’s of course secondary to the question of whether we are doing something we believe in,” he said about the paper’s image. “We’ve heard from noisy critics (mostly on the left) who are angry at Judy for earlier coverage, or angry because they suspect her source is someone they don’t approve of. But this is not, at bottom, about any one reporter or any one source. It’s about a principle. We’ve heard from others (mostly on the right) who disapprove of anything The Times does. But there’s also been a significant outpouring of support for her courage and our steadfastness.”

Keller also spoke to the questions surrounding what Miller’s assignment was at the time she learned Plame’s identity, but declined to spell it out. “While the questions of what Judy knew, and what she was working on, may be matters of general curiosity, the answers don’t touch the heart of the case,” he claims. “The question of what is going on with the case — meaning what the special prosecutor is up to, and why he seems to regard Judy as important to the case — is a mystery to me. It’s something I’d like to have answered — not just for our staff, but for our readers.”

The Times has been steadfast in its public support of Miller and persistent in calling for her release. Unlike Time magazine, which handed over the notes and e-mails of its reporter, Matthew Cooper, after he was subpoenaed in the same case, the Times stood behind Miller’s defiance of such an order. The Times editorial page on Aug. 8 even took to linking increased harassment of the press in other countries, like Nepal and Burundi, to Miller’s incarceration. An Aug. 15 editorial followed with a clear demand that Miller be freed, stating, “If she is not willing to testify after 41 days, then she is not willing to testify.”

Miller remains in jail at the Alexandria [Va.] Detention Center. Reports from visitors indicate she is holding up well, but has had some stomach problems related to jail food, misses the Internet and outside contact, and has had to withstand a constant stream of hip-hop videos on the communal television sets. She’s had no shortage of visitors, ranging from Keller to Tom Brokaw to Lucy Dalglish of the Reporters Committee for Freedom of the Press to one report of embattled United Nations ambassador-designate John Bolton getting face time with her behind bars.

Observes Times columnist Thomas Friedman, “People really support Judy and this principle.” Adds Nagourney, “I hope it works out for her.”

The Time cover story, written by Richard Behar and headlined “The Thriving Cult of Greed and Power,” called the church “a hugely profitable global racket” and described its intimidation methods as “Mafia-like.” The story was one of several by major news operations who took on the church with in-depth reports in the late 1980s and early 1990s. The Los Angeles Times launched a series that focused on Hubbard’s rise to power and the myths and distortions about his life — including bogus military claims and a dysfunctional relationship with his son. The series also looked at church marketing techniques and high-pressure tactics against members; accounts of former Scientologists about life in the church, which included the micromanagement of everything from careers to the preparation of baby food; and its counterattacks against critics, including the press and the IRS.

But several of the news outlets paid for their curiosity, either (like Time) through costly lawsuits or, according to reporters, personal harassment. In the intervening decade, there’s been a détente of sorts. What’s less clear is why. Has the church simply been more open to journalists — and less quick to take critical reporters to court? Or has the press simply shied away from potential court fights, especially at a time when many news outlets are cutting back on budgets and facing stronger competition in a growing media market?

It’s tough to dispute how aggressive the church has been in the past. Behar has said he had 10 lawyers and half a dozen private detectives following him as he researched the story, asking friends about his health and tax history. Joel Sappell, who co-wrote the June 1990 multipart series in the Los Angeles Times, recalled similar counterattacks. “They had private detectives follow us and they were rummaging through my past,” he recalls. “They have a real history of hardball and litigation.”

In addition to the libel suit, the church countered the Time story with a 12-week ad campaign in USA Today that summer. “This consisted of daily full-page advertisements and two full-color supplements,” says Ed Parkin, vice president of cultural affairs for the Church of Scientology. “It was so effective that we have heard from journalism professors that they have used it as a model in their university journalism classes.”

And while the Los Angeles Times was never sued for the series, the church bought up many billboards and bus ads in the L.A. area to counter the paper’s charges. “They even put a billboard at the end of my street, where I lived,” Sappell says. Other news organizations examined the church on everything from its tax-exempt status — which was granted in 1993 after a long fight with the IRS — to allegations of pilfering the savings of unsuspecting members and to cases of suicide by followers. Allegations by former Scientologists of being held captive were common, along with coverage of the church’s battles for recognition with government leaders in Germany and France.

Reporters have said the church fought back in other ways. In 1988, a St. Petersburg Times reporter accused the church of illegally obtaining his credit report, making obscene phone calls to his wife, and sending a private investigator after him. And in 1998, the Boston Herald reported that one of its writers had been pursued by a private detective after writing a five-part series on the church.

“There was a lot of negative coverage, and they had a policy that if you write something about the church that is incorrect or libelous, they will take you to court,” says J. Gordon Melton, director of the Institute for the Study of American Religion, who has observed the church for years. “They are very persistent.”

Scientology leaders also went after individuals and other groups seeking to expose their questionable doings, such as the Cult Awareness Network, which had targeted the church with public warnings for years and went bankrupt in 1996. It had been the subject of many suits from the church. (The CAN site was promptly snapped up by a Scientologist, and it now links to pieces sympathetic to the church — and disparaging to its critics.) The church maintains that reporters who truly made efforts to learn about Scientology have never been a problem. “Where reporters have taken the time to understand the Church and really get their questions answered, the public have been presented with an accurate view of Scientology,” Parkin said in a statement to Salon about press coverage. “Where reporters have not taken the trouble to understand who we are and what we are about, the public has been presented with an inaccurate view of Scientology. When this happens, it does the public a disservice.”

In recent years, however, the type of coverage the church has faced is decidedly different from the investigative reports of the early 1990s. Stories still refer skeptically to Scientology, but most of the coverage focuses primarily on celebrity members such as Tom Cruise and John Travolta. Any negative stories are usually limited to a specific church program under mild scrutiny, or to fans’ concerns that a celebrity, such as Cruise fiancée Katie Holmes, has unwittingly joined the flock. “My sense in general is that America increasingly blends entertainment with news, to the neglect of important news items involving Scientology, ” says Stephen Kent, a professor at the University of Alberta, who has written extensively on Scientology. But what caused this shift to more lightweight coverage? “The church has changed the way it conducts business,” Sappell says. “They are trying to be much more mainstream.”

Kent agrees, adding, “It may not want to continue its aggressive court action, [in order] to maintain its image as a [mainstream] religion.” Parkin maintains the church was no less open to the press in the past. “We have always been willing to work with the press to help them understand us,” Parkin responded when asked if the church had taken a different tone with reporters. “As the Church expands in the United States and around the globe, there is an increased interest in finding out about us. And we are responding to that interest.” But, he adds, “We have always tried to resolve disputes short of litigation. That was not always possible in earlier years when we were forced to go to court to defend our rights and the rights of our parishioners to freely practice their religion. But as we have won more and more victories, we have had to resort to the courts much less. Nowadays it is a very rare occurrence.”

For many reporters who have written recently about Scientology, cooperation couldn’t be better. “They are very media friendly and there is nothing you can’t ask them,” says Ken Baker, West Coast executive editor for US Weekly. Benjamin Svetkey, who recently interviewed Tom Cruise for Entertainment Weekly and who has interviewed Travolta in the past about Scientology, agreed. “I have never had a problem,” he said, adding that both men have been glad to speak about the church. “Nobody [from Scientology] has told me not to ask them about it. Nobody has been anything but friendly about it.” He goes on to say, “It’s kind of bizarre in some ways how they have been villainized.”

And Nanette Asimov of the San Francisco Chronicle found similar cooperation when she did report critically on the church’s Narconon program, a drug treatment effort that drew scrutiny when it was incorporated into San Francisco’s public schools. Because of the attention brought by Asimov’s series, the city banned the Scientology program from its schools; several other school districts in the state, including Los Angeles, followed. Nonetheless, Asimov says, “I found that they were always accessible and polite for the most part,” adding, “and eager to answer questions. Hostility wasn’t part of it.”

At the same time, she described church officials as “unlike anyone else I have ever interviewed” while reporting her stories. “I got more phone calls from them prior to publication than I have from anyone. ‘Nervous’ doesn’t begin to describe how they were.” (In preparing this series, Salon writers and editors have fielded frequent calls — and one office visit — from church officials.)

Though the church says otherwise, its kinder and gentler press image seems to be deliberate, according to observers. Having settled its last major lawsuit in 2002 — in which it had to pay former Scientologist Lawrence Wollersheim $8.6 million for mental abuse — the church appears to be focused more on improving its publicity and less on defensive retaliation.

In addition to seemingly open access to inquiring reporters, the church has even invited journalists on tours of facilities that give an inside view nearly unthinkable for probing reporters five or 10 years ago. “I think they have been able to make the case that lots of the stuff against them is reduced to a matter of opinion,” Melton said about the Scientology press coverage. Kent says the church’s use of its celebrity members as ambassadors also softens its image. “They increasingly use their celebrities in a newsmaking fashion,” he says. “They are public relations officers for Scientology, and part of their mission is to represent Scientology to the outside world and to other governments.” But are news outlets simply afraid of unleashing their investigative attack dogs in case legal action and harassment will follow?

Alice Chasan, senior editor at BeliefNet.com, which monitors religious issues and coverage, said Scientology spokespeople seem to be in greater supply, and a greater number of comments from the church. At the same time, the in-depth coverage is minimal. “There is less of that kind of investigative reporting going on. Clearly, the spate of lawsuits has had a chilling effect,” she says.

One recent example of aggressive reporting, however, comes from the Buffalo News, which ran a four-part series in late January and early February of this year.

The paper reported that the local Scientology church pressures some members to cut off contact from relatives critical of Scientology, uses “deceptive tactics” to recruit members, actively seeks acceptance by linking to local government leaders, and practices intimidation and harassment. The series also profiled former Scientologist Jeremy Perkins, a 28-year-old who stabbed his mother to death in a violent attack after he had — at the church’s urging — stopped taking psychiatric medication.

Staff writer Mark Sommer knew going in about the church’s litigious history. “I was aware of their past enough to be reluctant to delve in to that world, how intimidating they could be and anticipated the likelihood of being sued,” he said. “But I was not going to let that get in the way.” He said he received “veiled threats” from local Scientology leaders, but would not comment on them further.

He did say that he found few former Scientologists willing to speak on the record for fear of retaliation. He also noted several instances of church officials misleading him — then later admitting their false statements when presented with evidence. In one case, officials initially said Perkins, the man who killed his mother, had not been a member, Sommer said. He also said church officials denied writing a speech for the mayor of Buffalo that was read when he declared “Church of Scientology Day” in the city in 2003. The mayor confirmed they had.

“They have a storyline,” Sommer said. “They get frustrated if you don’t go along with it.” The reporter also noted that while the Scientologists were willing to provide him with all of the information for the stories he sought — and gave him a tour of the local church and facilities — they also tried to micromanage the reporting as much as possible. “They were in daily contact with the paper days before the series ran, with great concern over what would appear,” Sommer recalled. “We met with them, but we wouldn’t back off on the stories.”

This story has been corrected since it was originally published.