Amid all this murkiness one fact is plain:
The Times' present crisis stems from a persistent failure to uphold its own journalistic standards.

In case you have been bewildered by the Judith Miller affair, here's a quick guide:

On July 6, the New York Times' reporter went to jail, allegedly for protecting a source who had illegally leaked the identity of CIA agent Valerie Plame.

On Sept. 29, she was released, after agreeing to give "limited testimony" before a grand jury.

On Oct. 17, the Times published "A Notebook, A Cause, A Jail Cell, and A Deal," which, along with Miller's own account, was supposed to explain why she had so long attempted to conceal her conversations with Lewis "Scooter" Libby, Vice President Dick Cheney's chief of staff.

If you're still confused, it's not your fault: The Times has yet to unravel the mysteries surrounding this cloak-and-dagger case.

The Notebook: Miller testified that she has no idea why references to Plame appeared in notebooks she used while talking to Libby about Bush administration critic Joseph Wilson, who happens to be married to Plame. Miller will say only that Libby did not reveal Plame's identity.

A Cause: Since Miller still won't clarify her role, we still don't know if her aim was to advance the White House's push toward war, improve the Times' reputation, or restore her own public image after widespread criticism of her massive misreporting on weapons of mass destruction. (She had written articles implying the Saddam Hussein had them. He didn't.)

A Jail Cell: Since Miller got Libby off the hook -- at least until his indictment Friday -- by testifying that he had not outed Wilson's wife, we still don't know why she spent 85 days in jail, why she got out, or what other sources she used to learn more about Plame.

A Deal: Since even her editors apparently can't persuade her to come clean, we don't know if the deal Miller made was with the White House, the Times, or herself.

Amid all this murkiness one fact is plain: The Times' present crisis stems from a persistent failure to uphold its own journalistic standards. For example, after Miller's prize-winning but truth-losing reports on WMDs became too glaringly flawed to defend, her editors admitted that many of her articles were riddled with unfounded claims. In their apologetic note to readers, however, they did not identify Miller by name. Readers can determine whether this granting of anonymity conformed to the paper's current "Guidelines on Integrity," which state: "There can be no prescribed formula for (anonymous) attribution, but it should be literally truthful, and not coy."

The Times' decision to beatify Miller despite her misreporting on WMDs also obscured the impropriety inherent in her simultaneous hawking of "Germs," her best-selling book on bio-terrorism. Again, readers can judge whether ignoring Miller's self-serving exaggerations about unconventional weapons contradicted the Times' admonition to itself to be "vigilant in avoiding any activity that might pose an actual or apparent conflict of interest and thus threaten the newspaper's ethical standing."

In an overdue gesture of transparency, Times public editor Byron Calame acknowledged that Miller's troubling history might impede her transition back into the newsroom. However, Calame is, he admitted two weeks ago, still unable "to nail down... whether Ms. Miller holds a government security clearance." But while Miller now insists that she had the same security status as other embedded reporters, which would oblige her to share sensitive information only with high-level editors, here's what she told the grand jury about a breakfast meeting with Libby at the St. Regis Hotel in Washington, D.C.: "At our July 8 meeting I might have expressed frustration to Mr. Libby that I was not permitted to discuss with editors some of the more sensitive information about Iraq."

Miller seems to be implying that Libby could've relieved her vexation by allowing her to let her editors in on especially secret secrets. This suggests that her status was markedly different from that of other "embeds," not merely because it's hard to figure how a journalist who was dining with a high-level White House official in Washington could be simultaneously embedded in Iraq, but also because it gives us a pretty good hint that Libby was managing Miller's reporting. Otherwise, why would she expect him to free her to talk?

Perhaps Calame or someone else at the Times will "nail down" whether Miller is herself a government agent or whether her "security clearance" was her own invention. But if we can only speculate about what Calame might discover or Miller might have hidden, which is all we can do at this point, then we are left with one certainty: The Times has failed to live up to its pledge to "do nothing that might erode readers' faith and confidence in our news columns." In choosing to leave us guessing, the Times may have prolonged Miller's swan song as a heroic reporter, but it gave up its claim to our trust.