III: The Charges and What Followed
While it was a simple matter to fire Lee, it was altogether more difficult to charge him with espionage or any betrayal of US secrets, since there was absolutely no evidence. Lee had to be charged with something, but what? Once again, in an April 28, 1999, story, Gerth and Risen came through with the charge--again based on leaks from the ongoing investigation--that Lee had improperly downloaded computer files containing nuclear codes. This time their lead was even more frightening than the one in the first story: "A scientist suspected of spying for China improperly transferred huge amounts of secret data from a computer system at a government laboratory, compromising virtually every nuclear weapon in the United States arsenal, government and lab officials say."
In fact, the material that Gerth and Risen referred to as "secret data" was not classified as secret when Lee downloaded it; rather, it carried the low-level designation "protect as restricted data" (PARD), which meant it could be sent to colleagues through registered US mail. Some of the material was reclassified as "secret" after Lee's firing, but never as "top secret." As to "compromising virtually every nuclear weapon in the United States arsenal," that charge was dismissed as absurd by top weapons experts, who provided affidavits to Lee's defense attorneys. Former Los Alamos director Dr. Harold Agnew, a top adviser on nuclear weapons to five Presidents, testified that "if the People's Republic of China had already obtained these codes, or were to obtain these codes, it would have little or no effect whatsoever on today's nuclear balance."
When the government finally got around to arresting Lee, in December of 1999, it charged him only with the improper handling of files--and stretched to include the claim that the mishandling had been done "with the intent to injure the United States" and "secure an advantage to a foreign nation." But the indictment made no reference to the theft of the W-88 warhead data, which had led to his excoriation in the Times, and the prosecutors told the court they did not plan to make the case that Lee ever actually passed any secrets to a person or nation. (By contrast, former Director of Central Intelligence John Deutch, who downloaded some of the nation's top secrets to his home computer, has not yet been charged with any crime and remains a free man.)
For nine months after his arrest, Lee remained in prison without bail, while his attorneys mounted an aggressive effort to disprove the government's case against him. Finally, in August, after the lead FBI agent, Robert Messemer, admitted he'd misled the judge on several topics--including the claim that Lee had lied to a colleague to gain access to his computer--and witnesses came forward to say that much of the allegedly secret material was in the public domain, the judge agreed to bail for Lee.