Here’s how the Justice Department sources say the investigation came about:

When several news organizations sought Clinton’s file under the Freedom of Information Act, State officials, who went to retrieve it from the records center in suburban Maryland, found the file out of place. Although passport and personal files are protected by the Privacy Act, State always pulls the files to see if they contain any information that can be released. Officials say that inside Clinton’s file, they noticed staple holes on copies of the passport application, suggesting pages might have been torn out. Aware of the political implications, Assistant Secretary of State for Consular Affairs Elizabeth Tamposi immediately notified Under Secretary for Management John Rogers. He called in the department’s inspector general, Sherman Funk, and notified Acting Secretary of State Lawrence Eagleburger.

After a brief investigation, Funk recommended that the matter be turned over to the FBI. Eagleburger agreed, the sources say, and instructed State staffers not to discuss the investigation with anyone at the White House. Eagleburger put himself under the same restriction, telling aides he never raised it with White House chief of staff (and former secretary of state) James Baker. “We knew it could well turnout to be nothing, or a setup,” said a top State official. “But this was a sensitive enough case that the State Department should not be in the position of investigating itself” After the FBI started its investigation, NEWSWEEK learned of it while making other inquiries.

Government sources say the FBI quickly concluded that the holes in the file were not suspicious. They were most likely caused by the removal of such things as a photo and a bank cheek used to pay the application fee as part of the normal processing of documents, the sources say.

The FBI believes that the State Department acted “in good faith” when it requested the FBI investigation. Tamposi and Rogers are Bush-administration appointees. Tamposi was recommended for the post by GOP Sen. Warren Rudman of New Hampshire. Rogers is a longtime associate of Baker’s. Funk is a career civil servant with a reputation as a hardnosed IG.