WASHINGTON, April 10 — From the early days of the C.I.A. leak investigation in 2003, the Bush White House has insisted there was no effort to discredit Joseph C. Wilson IV, the man who emerged as the most damaging critic of the administration's case that Saddam Hussein was seeking to build nuclear weapons.

But now White House officials, and specifically President Bush and Vice President Dick Cheney, have been pitched back into the center of the nearly three-year controversy, this time because of a prosecutor's court filing in the case that asserts there was a strong desire by many, including multiple people in the White House, to undermine Mr. Wilson.

The new assertions by the special prosecutor, Patrick J. Fitzgerald, have put administration officials on the spot in a way they have not been for months, as attention in the leak case seems to be shifting away from the White House to the pretrial procedural skirmishing in the perjury and obstruction charges against Mr. Cheney's former chief of staff, I. Lewis Libby Jr.

Mr. Fitzgerald's filing talks not of an effort to level with Americans but of a plan to discredit, punish or seek revenge against Mr. Wilson. It concludes, It is hard to conceive of what evidence there could be that would disprove the existence of White House efforts to 'punish Wilson.'

With more filings expected from Mr. Fitzgerald, the prosecutor's work has the potential to keep the focus on Mr. Bush and Mr. Cheney at a time when the president is struggling with his lowest approval ratings since he took office.

Even on Monday, Mr. Bush found himself in an uncomfortable spot during an appearance at a Johns Hopkins University campus in Washington, when a student asked him to address Mr. Fitzgerald's assertion that the White House was seeking to retaliate against Mr. Wilson.

Mr. Bush stumbled as he began his response before settling on an answer that sidestepped the question. He said he had ordered the formal declassification of the 2002 National Intelligence Estimate on Iraq in July 2003 because it was important for people to get a better sense for why I was saying what I was saying in my speeches about Iraq's efforts to reconstitute its weapons program.

Mr. Bush said nothing about the earlier, informal authorization that Mr. Fitzgerald's court filing revealed. The prosecutor described testimony from Mr. Libby, who said Mr. Bush had told Mr. Cheney that it was permissible to reveal some information from the intelligence estimate, which described Mr. Hussein's efforts to acquire uranium.

But on Monday, Mr. Bush was not talking about that. You're just going to have to let Mr. Fitzgerald complete his case, and I hope you understand that, Mr. Bush said. It's a serious legal matter that we've got to be careful in making public statements about it.

Every prosecutor strives not just to prove a case, but also to tell a compelling story. It is now clear that Mr. Fitzgerald's account of what was happening in the White House in the summer of 2003 is very different from the Bush administration's narrative, which suggested that Mr. Wilson was seen as a minor figure whose criticisms could be answered by disclosing the underlying intelligence upon which Mr. Bush relied.

It turned out that much of the information about Mr. Hussein's search for uranium was questionable at best, and that it became the subject of dispute almost as soon as it was included in the 2002 National Intelligence Estimate on Iraq.

The answer to the question of whose recounting of events is correct — Mr. Bush's or Mr. Fitzgerald's — may not be known for months or years, if ever. But it seems there will be more clues, including some about the conversations between Mr. Bush and Mr. Cheney.

Mr. Fitzgerald said he was preparing to turn over to Mr. Libby 1,400 pages of handwritten notes — some presumably in Mr. Libby's own hand — that could shed light on two very different efforts at getting out the White House story.

One effort — the July 18 declassification of the major conclusions of the intelligence estimate — was taking place in public, while another, Mr. Fitzgerald argues, was happening in secret, with only Mr. Bush, Mr. Cheney and Mr. Libby involved.

Last week's court filing has already led the White House to acknowledge, over the weekend, that Mr. Bush ordered the selective disclosure of parts of the intelligence estimate sometime in late June or early July. But administration officials insist that Mr. Bush played a somewhat passive role and did so without selecting Mr. Libby, or anyone else, to tell the story piecemeal to a small number of reporters.

But in one of those odd twists in the unpredictable world of news leaks, neither of the reporters Mr. Libby met, Bob Woodward of The Washington Post or Judith Miller, then of The New York Times, reported a word of it under their own bylines. In fact, other reporters working on the story were talking to senior officials who were warning that the uranium information in the intelligence estimate was dubious at best.

Mr. Fitzgerald did not identify who took part in the White House effort to argue otherwise, but the evidence he has cited so far shows that Mr. Cheney's office was the epicenter of concern about Mr. Wilson, the former ambassador sent to Niger by the C.I.A. to determine what deal, if any, Mr. Hussein had struck there.

Throughout the spring and early summer of 2003, Mr. Fitzgerald concluded, the former ambassador had become an irritant to the administration, raising doubts about the truthfulness of assertions — made publicly by Mr. Bush in his State of the Union address in January of that year — that Iraq might have sought uranium in Africa to further its nuclear ambitions.

Mr. Wilson's criticisms culminated in a July 6, 2003, Op-Ed article in The Times in which he voiced the same doubts for the first time on the record. He cited as his evidence his 2002 trip to Niger, instigated, he said, because of questions raised by Mr. Cheney's office.

Mr. Wilson's article, Mr. Fitzgerald said in the filing, was viewed in the Office of the Vice President as a direct attack on the credibility of the vice president (and the president) on a matter of signal importance: the rationale for the war in Iraq.

Mr. Fitzgerald suggested that the White House effort was a plan to undermine Mr. Wilson.

Disclosing the belief that Mr. Wilson's wife sent him on the Niger trip was one way for defendant to contradict the assertion that the vice president had done so, while at the same time undercutting Mr. Wilson's credibility if Mr. Wilson were perceived to have received the assignment on account of nepotism, Mr. Fitzgerald's filing said.