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(CNN) -- CNN Justice Department Correspondent Pierre Thomas joined Law Chat at 12:30 p.m. Wednesday, September 13, to discuss the plea agreement between fired scientist Wen Ho Lee and federal prosecutors. Lee has been held in solitary confinement for nine months pending his trial on charges of charges of mishandling sensitive nuclear information while working at the Los Alamos National Laboratory in New Mexico. CNN.com provided a typist for Thomas. The following is an edited transcript of the chat:

CNN Host: Can you update us on the latest on the plea agreement for Los Alamos scientist Wen Ho Lee?

Pierre Thomas:Right now, lawyers for Wen Ho Lee and the government are meeting and are apparently very close to resolving the final details of his guilty plea. We should know in the next couple of hours for certain.

CNN Host: Did Wen Ho Lee unequivocally admit guilt with this agreement?

Pierre Thomas: He did. As part of the agreement, he is going to plea guilty to one felony count of mishandling classified information. The government is willing to drop 58 other counts and he would walk out a free man. However, Wen Ho Lee will have to cooperate with the government subject to lie detector tests and extensive questioning by the FBI. If it turns out that he lies about anything of major importance he would be subject to criminal prosecution.

Question from Debra: Has it been proven that Lee was giving away secrets?

Pierre Thomas: Interestingly, Wen Ho Lee was never charged with espionage in terms of passing secrets to anyone. And he maintains -- and the government has never found -- evidence that he in fact did give secrets to anyone.

Question from Spacebird: How did they arrive at mishandling information from the raft of espionage charges? Does the government just want to know who got the information, or was it a weak case to start with?

Pierre Thomas: Again they only charged him with mishandling classified information. And the charges specifically dealt with Lee secretly downloading nuclear information onto computer tapes. Several of the tapes are unaccounted for so the government wanted to do two things: One, get a conviction on illegally downloading the tapes and, two, to find out why he downloaded the tapes and what happened to them.

Question from humphrey: And for what purpose was he downloading this info on to tapes?

Pierre Thomas: That is the major mystery that we don't yet have an answer to. And the government basically decided that the national security interests were more important than the length of Lee's jail time, i.e., they need to know what happened to the information. Lee maintains that he didn't give it to anyone and that he destroyed the tapes.

Question from James01: In your opinion, will he walk out unscathed?

Pierre Thomas: I try to not have opinions on what I cover, but the key will be to follow to the degree we can what he tells the government during his cooperation. But clearly if this deal is signed, sealed and approved by a court today Wen Ho Lee will go from facing life in prison to being a free man.

Question from PDR: What can you say about the handling of the case by the FBI? They seemed not to grasp what is classified and what isn't?

Pierre Thomas: The whole case began with allegations of Chinese espionage and . . . there are some people who believe that the FBI targeted Wen Ho Lee because he's Asian American. The government flatly denies that claim and said while they could find no evidence that Lee had committed espionage, they did find evidence that he was downloading these tapes and putting them in the position that was vulnerable.

Question from Debra: There have been accusations from the Republicans that this incident reflects neglect of a Democrat administration. Is there merit to this accusation?

Pierre Thomas: Well clearly evidence has shown that there were serious security flaws at the Los Alamos Nuclear Weapons Laboratory. And there have been a whole slew of proposals both from the Energy Department and from Congress to tighten up security at the nuclear weapons labs.

Question from SpelmiN: Why nine months a free man and then deemed so dangerous to be put in solitary?

Pierre Thomas: The government argued that until they could find out what happened to the missing tapes that Lee was potentially a threat in terms of providing the information to enemies of the United States.

Question from Spacebird: Does the evidence support the Republican assertion that it was just this administration, or does it indicate a long-standing bipartisan history of lax security?

Pierre Thomas: The Democrats say that this lack of security at the Nuclear Weapon Labs goes back to Republican and Democratic administrations. The Republicans say that the problems became worse under the Clinton administration. Who do you believe? Well that's a subject of debate.

Question from SkepticLou: Will the former CIA director, charged with similar crimes, also be placed in solitary for eight months? I think this is a classic case of a Justice Department "do as we say, not as we do".

Pierre Thomas: Well, Lee's supporters have long maintained that Lee was being treated unfairly. There have been other cases like the former CIA director where sensitive information was mishandled and the person was not prosecuted. And they felt that Lee was a victim of selective prosecution. Having said that, the former CIA director is now under criminal investigation and the Justice Department is weighing whether to charge him.

Question from Debra: What is meant by the term "secret"? Was he sloppy or slinking around?

Pierre Thomas: Again, that's the great mystery here. Was Wen Ho Lee being the absent-minded professor? Or was something else going on?

CNN Host: Do you have any final thoughts for our audience?

Pierre Thomas: The Wen Ho Lee story is an extremely complicated one. Did the government overreach? Why did he download this information? Was the information vulnerable to U.S. adversaries? Many questions that have yet to be fully answered. But we'll keep digging to find out.