A federal grand jury indicted him on charges of stealing secrets about the U.S. nuclear arsenal for the People's Republic of China (PRC) in December 1999.[1] After federal investigators were unable to prove these initial accusations, the government conducted a separate investigation. Ultimately it charged Lee only with improper handling of restricted data, one of the original 59 indictment counts, a felony count. He pleaded guilty as part of a plea settlement.
He filed a civil suit that was settled. In June 2006, Lee received $1.6 million from the federal government and five media organizations as part of a settlement leaking his name to the press before any charges had been filed against him.[2]