From Saturday's New York Times:

And when the prosecutor in the case asked her to explain how "Valerie Flame" appeared in the same notebook she used in interviewing Mr. Libby, Ms. Miller said she "didn't think" she heard it from him. "I said I believed the information came from another source, whom I could not recall."

After an 85-day moral stand in prison and two weeks of silence from the NYT, Judith Miller, who made much of the fact that she did not even write a story on the subject, had two clear references to Valerie Plame in her notes, "Valerie Flame" and later "Valerie Wilson" -- and she claims she has no idea who she heard them from.*

The Times ran its long-promised story on Saturday, "The Miller Case: A Notebook, a Cause, a Jail Cell and a Deal," put together by the NYT's investigative team of Don Van Natta Jr., Adam Liptak, Clifford J. Levy and Janny Scott under the supervision of NYT deputy managing editor Jon Landman. The 5,800-word article sadly makes clear the stranglehold Judith Miller had over the Times, the lack of cooperation she offered, and the failure of Times leadership to control the situation (Jay Rosen, right on all counts.)

You can't help but feel bad for the New York Times: its leadership impugned, its staffers divided, its morale low, its reporters scooped regularly on its own story.

And meanwhile, Judith Miller, after incurring millions in legal fees, let her colleagues at the Times down in the most fundamental way: she refused to talk to them. "In two interviews," wrote the Times, "Ms. Miller generally would not discuss her interactions with editors, elaborate on the written account of her grand jury testimony or allow reporters to review her notes." A far cry from the story promised by Bill Keller, the story that they were "yearning" to write now that Miller had been released from her contempt charge.

But Keller had promised something he couldn't deliver; Judy was the one making the decisions, and she was making them alone:

But Mr. Sulzberger and the paper's executive editor, Bill Keller, knew few details about Ms. Miller's conversations with her confidential source other than his name. They did not review Ms. Miller's notes. Mr. Keller said he learned about the "Valerie Flame" notation only this month. Mr. Sulzberger was told about it by Times reporters on Thursday.

Interviews show that the paper's leaders, in taking what they considered to be a principled stand, ultimately left the major decisions in the case up to Ms. Miller, an intrepid reporter whom editors found hard to control.

They threw their money, editorial voice and critical support in the newsroom behind Judith Miller, and she threw the barest minimum back, even turning her copy in late so that the all-important investigative story missed the deadline for the paper's "bulldog" edition.

The picture that emerges is of a headstrong reporter who felt she could make her own rules (her description of herself as "Miss Run Amok" seems accurate), and an institution that failed to take control of its own story -- potentially a story with far-reaching implications into the highest levels of government. Ouch.

Some highlights:

Miller "would not discuss her sources" other than Scooter Libby, and claimed not to remember the source of the "Valerie Flame" name.

Keller actively took her off the WMD beat in July 2003, but she kept on "drifting on her own back into the national security realm." No one appeared to be directly in charge of her.

The Times' top management kept the identity of Miller's source to themselves; "[e]ven after reporters learned it from outside sources, the Times did not publish Mr. Libby's name, though other news organizations already had."

Miller told the Grand Jury that she interpreted Scooter Libby's letter mentioning how no reporters had discussed Plame with him "might be perceived as an effort by Mr. Libby to suggest that I, too, would say we had not discussed Ms. Plame's identity. Yet my notes suggested that we had discussed her job." Libby's lawyer apparently told Miller "don't go there" [Libby's complicity] about Libby during testimony.

Miller agreed to identify Libby as a "former Hill staffer" rather than a "senior administration official," which

Miller claimed that the "Aspens are turning" line was in reference to her running into Libby all decked like a cowboy and hadn't recognized him. I'm not buying it; it looks like Libby's a guy with lots to lose, and that purple prose smacks of some sort of deeper messge.

Miller is on a leave of absence from the Times and "hopes to return to the newsroom." There are many that hopes she does not. Oh yes, and guess what? Turns out she is writing a book. Huh. You don't say.

The Miller Case: A Notebook, a Cause, a Jail Cell and a Deal [NYT]
My Four Hours Testifying in the Federal Grand Jury Room [NYT]

Related:
Judith Miller and the New York Times: Comprehensive Coverage [PressThink]
Arianna Huffington on Judy Miller [HuffPo]
NY Times Publishes Devastating Article on Judith Miller Case, While Revealing Newsroom Controversy (plus links) [E&P]
Judy Miller and the damage done [Salon]
The Times Gives Us a Modified, Limited Hangout [CJR]
Miller's Weak-end [FishbowlDC]
The NYT Miller Revelations [Kausfiles](note his point on how Miller may actually have made it easier for the gov't to send reporters to jail!)

Additional Fishbowl Coverage:

Judith Miller: Thoughts from the Armchair Critics

Judith Miller: Clues in "Hard News"

Switched at Birth? Judith Miller and Dawn Eden

Judith Miller: Postscript to the Postscript

*As Farhad Manjoo points out in Salon, this does not necessarily exonerate Libby; it is still pretty clear that they discussed the fact that Wilson's wife worked for the CIA. Furthermore, Manjoo argues that Miller's testimony lays the foundation for Libby to be charged with either (or both) of breaking espionage law or obstruction of justice. Gulp. Not looking great for Libby!