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For months, he called it an honest mistake.

But on Friday, Sandy Berger (search) pleaded guilty to a misdemeanor in federal court. Berger, who served as President Clinton's national security adviser, is acknowledging that it wasn't an honest mistake and that he intentionally took and destroyed copies of classified documents from the National Archives (search) and cut them up with scissors.

Berger acknowledged to U.S. Magistrate Deborah Robinson that he intentionally took and deliberately destroyed three copies of the same document dealing with terror threats during the 2000 millennium (search) celebration. He then lied about it to Archives staff when they told him the documents were missing.

"Guilty, your honor," Berger responded when asked how he pleaded.

Robinson did not ask Berger why he cut up the materials and threw them away at the Washington office of his Stonebridge International consulting firm. Berger, accompanied by his wife, Susan, did not offer an explanation when he addressed reporters outside the federal courthouse following the hearing.

"It was a mistake and it was wrong," he said, refusing to answer questions.

It's part of a plea agreement between Berger — who still claims he hasn't done anything criminally wrong — and the Justice Department so he doesn't get jail time.

Noel Hillman, chief of the Justice Department's public integrity section, would not discuss Berger's motivation, but said the former national security adviser understood the rules governing the handling of classified materials. Berger only had copies of documents; all of the originals remain in the government's possession, Hillman said.

The charge of unauthorized removal and retention of classified material is a misdemeanor that carries a maximum sentence of a year in prison and up to a $100,000 fine.

However, under a plea agreement that Robinson must accept, instead of jail, Berger would pay a $10,000 fine, surrender his security clearance for three years and cooperate with investigators. Security clearance allows access to classified government materials.

Berger was released and sentencing was set for July 8.

After his court appearance, Berger told reporters that he "excerised poor judgement" and "deeply regretted it." He said his motivation was to help himself and others prepare for their appearance before the commission probing the events surrounding the Sept. 11, 2001 attacks.

The U.S. District Court appearance was the culmination of a bizarre episode in which the man who once had access to the government's most sensitive intelligence was accused of sneaking documents out of the Archives, which houses the Constitution, Declaration of Independence and other cherished and top-secret documents.

The Bush administration disclosed the investigation in July, just days before the Sept. 11 commission issued its final report. Democrats claimed the White House was using Berger to deflect attention from the harsh findings, with their potential for damaging President Bush's re-election prospects.

After news of the probe surfaced, Berger admitted that twice during 2003, he knowingly removed classified documents regarding the government's anti-terror efforts and notes from the National Archives Annex in College Park, Md., by putting the papers in his jacket, his pants and in a leather case. That's a misdemeanor that can bring a maximum sentence of a year in prison and a $100,000 fine.

He said he was reviewing the materials to help determine which Clinton administration documents to provide to the independent commission investigating the Sept. 11 terror attacks. He called the episode "an honest mistake" and said he "deeply regrets" taking the material.

According to a statement released by the Justice Department on Friday, Berger took the documents to his office in Washington, where he destroyed three of the copies. Soon after he visited the Archives in October 2003, building officials discovered that documents were missing and, two days later, contacted Berger.

Initially, Berger did not tell the Archives staff that he had taken the documents but later that night told Archives staff that he had "accidentally misfiled" two of them, according to the Justice Department. The next day, he returned to Archives staff the two remaining copies of the five documents he had taken during the September and October visits. Each of the five copies of the document was then given to the Sept. 11 commission.

"In his plea, Berger also admitted that he concealed and removed his handwritten notes from the Archives prior to a classification review, in violation of Archives rules and procedures," reads the DOJ statement. "Those notes have been returned to the government."

But still missing are drafts of a sensitive after-action report on the Clinton administration's response to a failed terror plot to blow up the Los Angeles International Airport during December 1999, otherwise known as "the Millennium plot."

One source told FOX News that the report was critical of how the Clinton administration handled Al Qaeda threats to the U.S. homeland and that the missing report made security recommendations that were never implemented.

The Associated Press first reported in July that the Justice Department was investigating Berger for incidents at the Archives the previous fall. The disclosure prompted Berger to step down as an adviser to the campaign of Democratic presidential candidate John Kerry.

Clinton was among Democrats who questioned the timing of the disclosure of the Berger probe, three days before the release of the final Sept. 11 commission report. The commission, writing three months before the 2004 presidential election, detailed failures of both the Clinton and Bush administrations.

Clinton was among the Democrats who questioned the timing of the disclosure of the Berger probe three days before the release of the Sept. 11 report. Leaders of the Sept. 11 commission (search) said they were able to get every key document needed to complete their report.

FOX News' Bret Baier, Anna Persky and The Associated Press contributed to this report.