ALBUQUERQUE, N.M. â€“ Soon after Wen Ho Lee raised his right arm in federal court and pleaded guilty to one felony count of inappropriately downloading nuclear weapons secrets at Los Alamos National Laboratory, the judge presiding over the case admonished the Clinton administration for what he labeled an "embarrassment."
"It is only the top decision makers of the executive branch who have caused embarrassment by the way this case began and was handled," U.S. District Judge James Parker said before a packed courtroom Wednesday afternoon. "They have embarrassed the entire nation."
Then Judge Parker, a Republican appointed by former President Ronald Reagan, looked directly at the diminutive, gray-haired computer scientist and apologized.
"In my opinion, you've been punished harshly," the judge said, adding that citizens usually are entitled to be released until they are tried and convicted. "You lost valuable rights as a citizen. I am sad that I was induced in December to order your detention."
Soon after, a smiling Dr. Lee stepped out of the courthouse a free man.
"I am very happy to go home with my wife and my children," said Dr. Lee, 60, who also publicly thanked supporters. "For the next few days, I'm going fishing."
When he finally returned to his red home in White Rock, Dr. Lee was greeted by dozens of friends and neighbors waving U.S. flags and placards.
"You won!!!" read one sign.
"Welcome home to your town, your garden and Mozart," said another handwritten poster, dedicated to the quiet man with a passion for gardening and classical music. At his homecoming celebration, Dr. Lee was visibly moved by the show of support.
"I'm so impressed to see such a big crowd here, you know?" Dr. Lee told friends at the celebration held at his neighbor's house. "I think I survived."
But Dr. Lee's involvement isn't over.
As part of the plea agreement that reduced the number of felonies from 59 to one, Dr. Lee will have to undergo as much as 60 hours of grueling interrogation from federal agents over the fate of seven of 10 tapes in which he downloaded nuclear data.
The sessions will begin Sept. 26 and will run for six hours a day for 10 days. Dr. Lee also will make himself available for further debriefing sessions, if necessary. And he will allow authorities to search his home or any other storage spaces, such as safe deposit boxes, if questioning leads to that. The deal further stipulates that Dr. Lee could be required to take polygraph exams on issues related to national security.
Though the federal government's case largely collapsed, Attorney General Janet Reno in Washington contended that her agency had won a victory in deepening the questioning of Dr. Lee.
"In accepting the plea offer, we now, for the first time, have an opportunity to determine what Dr. Lee did with the tapes â€“ something he has repeatedly refused to tell us since April 1999," Ms. Reno said in a statement.
"We saw this plea agreement as the best chance to find out where those tapes are, where they have been and who else has had access to them, if anyone," she said. "Had this case proceeded to trial, and we prevailed, Dr. Lee would have faced many years in prison. But we might never have learned what happened to the tapes."
The U.S. Department of Energy issued a much terser statement: "Dr. Lee pled guilty to a felony, admitting that he mishandled sensitive classified information. That speaks for itself."
While the deal protects Dr. Lee from prosecution resulting from testimony by the prosecutors in this case, it left open the possibility of other agencies coming after him. The immunity restriction in the agreement is limited to the U.S. Department of Justice and New Mexico.
"Is it possible that any other authority will be in a position to prosecute Dr. Lee?" Judge Parker asked attorneys.
"Anything is possible, Judge," responded George Stamboulidis, assistant U.S. attorney. "But the agreement is the agreement."
Dr. Lee's attorney Mark Holscher said: "We have absolute confidence that if something arises, we will take care of it."
Prosecutors declared a victory in the case, despite the terse comments from the judge.
"This is a fair result, right result and, most important, helps protect national security," said Norman Bay, U.S. attorney for New Mexico. "Why did Dr. Lee make the tapes? What did he do with them? Does anybody else have them? Now, we'll know.
"If he lies, the government can move to set aside the plea agreement and prosecute for perjury," Mr. Bay said.
"This case has been about national security, not about the longest possible sentencing that could be imposed on Dr. Lee."
Standing before the judge with his attorneys beside him, Dr. Lee admitted that in 1994 he had unauthorized possession of documents related to national defense.
"I used an unsecure computer ... to download a document related to national defense," Dr. Lee said. "I knew at the time that my position ... was unauthorized and that under the Los Alamos National Laboratory directives I was not permitted" to have the documents outside of the secured perimeter.
Dr. Lee also acknowledged that the government had national security reasons for the prosecution.
The defense had argued that the Taiwan-born Dr. Lee was the victim of racial profiling because he is ethnic Chinese. The government expressed concern that Dr. Lee may have provided a third party, possibly China, with information about a top U.S. nuclear weapon. Prosecutors later abandoned that suspicion but maintained that he had mishandled secrets.
The felony conviction carries a maximum penalty of 10 years' imprisonment, a fine of $250,000 and up to three years of supervised release. The scientist instead was credited with time already served â€“ 278 days in solitary confinement.
In exchange, Dr. Lee will have to tell prosecutors how, when and where the copies of the data were made and the manner in which they were disposed of. He also has submitted a written declaration that he never shared, nor had any intention of sharing, the information with any other source.
Judge Parker asked Mr. Stamboulidis to explain why it was now in the best interest of the nation to accept the plea agreement.
"It gives us the best chance to find out, in confidence, precisely what happened to the tapes," Mr. Stamboulidis said. "The location of the tapes was always our primary concern."
He added that this penalty also sent a message to others who work on nuclear weapons "that they not violate that sacred trust for any reason, as unfortunately happened here."
Judge Parker said that he was perplexed by the government agreement to let Dr. Lee out after such an aggressive prosecution. He said that throughout court proceedings, he was told two things:
First, "that the decision to prosecute you was made at the highest levels of the executive branch in Washington, D.C.," and, second, "that the decision to prosecute you was made personally by the president's attorney general."
Judge Parker added, "The executive branch has enormous power, the abuse of which can be devastating to our citizens."
He added that although he thought the nine-month confinement was "not unjust," Dr. Lee was "terribly wronged" to be held in "demeaning, unnecessarily punitive conditions."
Judge Parker said that for that, he was "truly sorry."
As the hearing in the complex national security case came to an end, Dr. Lee's 26-year-old daughter, Alberta, said with a heavy sigh: "Finally, my life can go on. I can breathe."
Life in Dr. Lee's community hasn't been the same since March 1999, when he was publicly labeled an espionage suspect and fired from his job at the lab.
Many in the White Rock neighborhood have criticized the way federal agents swarmed the area with surveillance cameras.
Prosecutors maintain that the crime to which he pleaded guilty was serious, and they defended their investigative tactics.
"Which American would want us to ignore somebody making their own private library of nuclear data?" Mr. Stamboulidis said. "You'd want us to pounce and to be aggressive, and we did just that."
Staff writer Robert Dodge in Washington contributed to this report.