Last Oct. 2, former Clinton national security adviser Samuel R. "Sandy" Berger stayed huddled over papers at the National Archives until 8 p.m.

What he did not know as he labored through that long Thursday was that the same Archives employees who were solicitously retrieving documents for him were also watching their important visitor with a suspicious eye.

After Berger's previous visit, in September, Archives officials believed documents were missing. This time, they specially coded the papers to more easily tell whether some disappeared, said government officials and legal sources familiar with the case.

The notion of one of Washington's most respected foreign policy figures being subjected to treatment that had at least a faint odor of a sting operation is a strange one. But the peculiarities -- and conflicting versions of events and possible motives -- were just then beginning in a case that this week bucked Berger out of an esteemed position as a leader of the Democratic government-in-waiting that had assembled around presidential nominee John F. Kerry.

As his attorneys tell it, Berger had no idea in October that documents were missing from the Archives, or that archivists suspected him in the disappearance. It was not until two days later, on Saturday, Oct. 4, that he was contacted by Archives employees who said that they were concerned about missing files, from his September and October visits. This call -- in Berger's version of the chronology, which is disputed in essential respects by a government official with knowledge of the investigation -- was made with a tone of concern, but not accusation.

Berger, his attorney Lanny Breuer said, checked his office and realized for the first time that he had walked out -- unintentionally, he says -- with important papers relating to the Clinton administration's efforts to combat terrorism.

Berger alerted Archives employees that evening to what he had found. The classified documents were sensitive enough that employees arrived on a Sunday morning to pick them up.

Several days later, after he had retained Breuer as counsel, Berger volunteered that he had also taken 40 to 50 pages of notes during three visits to the Archives beginning in July, the lawyer said. Berger turned the notes over to the Archives. He has acknowledged through attorneys that he knowingly did not show these papers to Archives officials for review before leaving -- a violation of Archives rules, but not one that he perceived as a serious security lapse.

By then, however, Archives officials had served notice that there were other documents missing. Despite searching his home and office, Berger could not find them. By January, the FBI had been brought in, and Berger found himself in a criminal investigation -- one that he chose not to tell Kerry's campaign about until this week.

But three days after the disclosure of the Berger investigation, many of the basic facts of the controversy remain unknown or are contested, as well as more subjective questions about how seriously his lapse should be regarded or its effect on politics this year.

A government official with knowledge of the investigation said Archives employees took action promptly after noticing a missing document in September. This official said an Archives employee called former White House deputy counsel Bruce Lindsey, who is former president Bill Clinton's liaison to the National Archives. The Archives employee said documents were missing and would have to be returned.

Under this version of events -- which Breuer denied -- documents were returned the following day from Berger's office to the Archives. Not included in these papers, the government official said, were any drafts of the document at the center of this week's controversy.

The documents that Berger has acknowledged taking -- some of which remain missing -- are different drafts of a January 2000 "after-action review" of how the government responded to terrorism plots at the turn of the millennium. The document was written by White House anti-terrorism coordinator Richard A. Clarke, at Berger's direction when he was in government.

Lindsey, now in private legal practice in Little Rock, did not return telephone and e-mail messages.

The government source said the Archives employees were deferential toward Berger, given his prominence, but were worried when he returned to view more documents on Oct. 2. They devised a coding system and marked the documents they knew Berger was interested in canvassing, and watched him carefully. They knew he was interested in all the versions of the millennium review, some of which bore handwritten notes from Clinton-era officials who had reviewed them. At one point an Archives employee even handed Berger a coded draft and asked whether he was sure he had seen it.

At the end of the day, Archives employees determined that that draft and all four or five other versions of the millennium memo had disappeared from the files, this source said.

This source and another government official said that archivists gave Berger use of a special room for reviewing the documents. He was examining the documents to recommend to the Bush administration which papers should be released to the commission investigating the Sept. 11, 2001, attacks. Archives spokeswoman Susan Cooper said that employees closely monitor anyone cleared to review classified presidential materials.

The contradictions over essential facts, such as when Berger was first alerted to missing documents, have characterized the controversy this week.

Sources have told The Washington Post, and other news organizations, that Berger was witnessed stuffing papers into his clothing. Through attorneys and spokesmen, Berger has denied doing that.

Berger has known for months that he was in potential jeopardy. Breuer was hired in October, and in January former White House press secretary Joe Lockhart was enlisted to remain on standby if a public controversy blossomed. But Berger allies said he did not inform Kerry because he had resolved to work privately with Justice Department officials, and received assurances that these officials would treat the matter confidentially.

The controversy is likely to continue, even after Berger relinquished his role as informal Kerry adviser on Tuesday. House Government Reform Committee Chairman Thomas M. Davis III (R-Va.) said yesterday that he plans an investigation.

"These allegations are deeply troubling, and it's our constitutional responsibility to find out what happened and why," Davis said in a statement. "It boggles the mind to imagine how a former national security advisor walked off with this kind of material in his pants, or wherever on his body he carried it. At best, we're looking at tremendously irresponsible handling of highly classified information -- some of which, I understand, has not yet been located."

White House press secretary Scott McClellan said that "a few individuals" in the White House counsel's office knew about the investigation before news reports.

There was bitterness among Berger allies this week in the timing of the disclosure and the wealth of detail -- inaccurate detail, they say -- about the allegations.

"This is a terrible experience for him, and he's embarrassed by his mistakes," Lockhart said, "but I think he also feels a sense of injustice that after building a reputation as a tireless defender of his country that many Republicans would try to assassinate his character to pursue their own ends."

Sandy Berger says he inadvertently removed papers from the National Archives.