THE good news is that the bad news didn't stop The New York Times from publishing a lengthy front-page article last Sunday about the issues facing Judith Miller and the paper, or from pushing Ms. Miller to give readers a first-person account of her grand jury testimony.

The details laid out in the commendable 6,200-word article by a special team of reporters and editors led by the paper's deputy managing editor answered most of my fundamental questions. At issue, of course, was Ms. Miller's refusal to divulge her confidential sources to the grand jury investigating who had leaked the identity of a C.I.A. undercover operative. But the article and Ms. Miller's account also uncovered new information that suggested the journalistic practices of Ms. Miller and Times editors were more flawed than I had feared.

The Times must now face up to three major concerns raised by the leak investigation: First, the tendency by top editors to move cautiously to correct problems about prewar coverage. Second, the journalistic shortcuts taken by Ms. Miller. And third, the deferential treatment of Ms. Miller by editors who failed to dig into problems before they became a mess.

To begin considering the handling of Ms. Miller and this whole episode, it is necessary to step back more than two years. Ms. Miller may still be best known for her role in a series of Times articles in 2002 and 2003 that strongly suggested Saddam Hussein already had or was acquiring an arsenal of weapons of mass destruction. Howell Raines was then the executive editor of The Times, and several articles about weapons of mass destruction were displayed prominently in the paper. Many of those articles turned out to be inaccurate.

By the spring of 2003, the newsroom was overwhelmed by the Jayson Blair fiasco, and Mr. Raines and the managing editor, Gerald Boyd, left the paper. When Bill Keller became executive editor on July 30, 2003, he focused on dealing with the trauma of the Blair scandal. Nevertheless, with questions growing about weapons in Iraq, he told Ms. Miller she could no longer cover those issues. But it took until May 2004 - more than a year after the war started and about a year after it became clear that there were no weapons of mass destruction in Iraq - before The Times acknowledged in an editors' note that the coverage was flawed. Mr. Keller then directed her to stay away from all national security issues.

Mr. Keller acknowledged to me last week that his tendency to act slowly in response to criticisms about prewar coverage might have contributed to the dismay among readers and in the newsroom with the way The Times dealt with protecting Ms. Miller's confidential sources in the leak investigation.

"By waiting a year to own up to our mistakes," Mr. Keller wrote Wednesday in response to questions I had asked, "I allowed the anger inside and outside the paper to fester. Worse, I fear I fostered an impression that The Times put a higher premium on protecting its reporters than on coming clean with its readers. If I had lanced the W.M.D. boil earlier, I suspect our critics - at least the honest ones - might have been less inclined to suspect that, THIS time, the paper was putting the defense of the reporter above the duty to its readers."

Mr. Keller is right. The paper should have addressed the problems of the coverage sooner. It is the duty of the paper to be straight with its readers, and whatever the management reason was for not doing so, the readers didn't get a fair shake.

The most disturbing aspect of the Oct. 16 retrospective was its revelation of the journalistic shortcuts that Ms. Miller seems comfortable taking.

One ethical problem emerged when Patrick Fitzgerald, the special prosecutor, asked Ms. Miller if she had pursued an article about Valerie Plame, the C.I.A. operative, or her husband, Joseph C. Wilson IV. Ms. Miller said in an interview for the retrospective that she "made a strong recommendation to my editor" that a story be pursued. "I was told no."

But Jill Abramson, now a managing editor and the Washington bureau chief in 2003, would have known about such a request. Ms. Abramson, to whom Ms. Miller reported, strongly asserted to me that Ms. Miller never asked to pursue an article about the operative. Ms. Abramson said that she did not recall Ms. Miller ever mentioning the confidential conversations she had with I. Lewis Libby, the vice president's chief of staff, who appears to be in the middle of the leak investigation. When I asked her, Ms. Miller declined to identify the editor she dealt with.

If Ms. Abramson is to be believed, and I do believe her, this raises clear issues of trust and credibility. It also means that because Ms. Miller didn't let an editor know what she knew, Times readers were deprived of a potentially exclusive look into an apparent administration effort to undercut Mr. Wilson and other critics of the Iraq war.

The negotiation of an attribution for a conversation that Ms. Miller had with Mr. Libby is also bothersome. She mentioned in her first-person account last Sunday that, to get Mr. Libby to give her certain information about the Plame situation, she had agreed to identify him as "a former Hill staffer" rather than the usual "senior administration official." She went on: "I agreed to the new ground rules because I knew that Mr. Libby had once worked on Capitol Hill."

When I talked to Ms. Miller, she dismissed concern about her agreement. She intended to get the information confirmed elsewhere before using it, she said, and would never have allowed Mr. Libby to be identified in print that way.

ANOTHER troubling ethical issue that I haven't yet been able to nail down is whether Ms. Miller holds a government security clearance - something that could restrict her ability to share with editors the information she gathers. During the Iraq war, Ms. Miller said in her personal account, "The Pentagon had given me clearance to see secret information as part of my assignment 'embedded' with a special military unit hunting for unconventional weapons."

But a Times article Thursday reported that Ms. Miller had said what she had signed was a so-called nondisclosure form, with some modifications. She indicated that under the conditions set by the commander of the unit she accompanied in Iraq, she had been allowed to discuss her most secret reporting only with Mr. Raines and Mr. Boyd.

The Times needs to review Ms. Miller's journalistic practices as soon as possible, especially because she disputes some accounts of her conduct that have come to light since the leak investigation began. Since Ms. Miller did the Plame-leak reporting, the paper has made a significant effort to be as upfront as possible with readers about anonymous sources. An update of the rules for the granting of anonymity in The Times's ethics guidelines by Allan M. Siegal, the standards editor, may also be a good idea.

The apparent deference to Ms. Miller by Arthur Sulzberger Jr., the publisher, and top editors of The Times, going back several years, needs to be addressed more openly, especially in view of the ethics issues that have come to light.

The freedom Ms. Miller was given to shape the legal strategy may have stemmed in part from the failure of top editors to dig into the case earlier in the battle.

Last Sunday's article raised this issue: "This car had her hand on the wheel because she was the one at risk," Mr. Sulzberger said. When I asked him this week if the integrity of The Times and the First Amendment weren't also at risk, he stressed that his assertion had to be read in the proper context. He referred me to his comments in a separate interview with The Times, which weren't published: "There were other hands on the wheel as well. And obviously if we felt that the situation didn't warrant the kind of support we gave her, we would have interceded."

Mr. Sulzberger, inclined by instinct and Times tradition to protect any reporter's confidential sources, wasn't doing anything special in backing Ms. Miller on this journalistic principle. But in an interview for the retrospective last Sunday, Ms. Miller acknowledged Mr. Sulzberger's special support in this case. "He galvanized the editors, the senior editorial staff. ... He metaphorically and literally put his arm around me," she said.

Neither Mr. Keller nor the publisher had done much digging into Ms. Miller's contacts with any of her confidential sources about Ms. Plame before the subpoena arrived on Aug. 12, 2004. Neither had reviewed her notes, for instance. Mr. Keller also didn't look into whether Ms. Miller had proposed a story about the Plame leak to an editor.

"I wish that when I learned Judy Miller had been subpoenaed as a witness in the leak investigation, I had sat her down for a thorough debriefing, and followed up with some reporting of my own," he wrote to me, adding later, "If I had known the details of Judy's engagement with Libby, I'd have been more careful in how the paper articulated its defense."

What does the future hold for Ms. Miller? She told me Thursday that she hopes to return to the paper after taking some time off. Mr. Sulzberger offered this measured response: "She and I have acknowledged that there are new limits on what she can do next." It seems to me that whatever the limits put on her, the problems facing her inside and outside the newsroom will make it difficult for her to return to the paper as a reporter.

The public editor serves as the readers' representative. His opinions and conclusions are his own. His column appears at least twice monthly in this section.

Commentary:
I never thought I'd say it. It's a very good start.