The FBI first became suspicious of Lee in 1982 while at Los Alamos National Laboratory. Lee repeatedly transferred top-secret computer files from a classified system at the lab into an insecure system beginning in 1983. The year before, the FBI sent Lee on an undercover mission to Lawrence Livermore National Laboratory near San Francisco after an FBI wiretap in 1982 overheard Lee telephone a Livermore scientist "who was rumored to be facing disciplinary action for delivering a scientific paper in Taiwan." At the time, Lee was considering delivering a paper in Taiwan. Lee was investigated for allegedly passing classified information to China that helped Beijing explode a neutron bomb in 1981. The scientist later was fired from Livermore but was never charged.

The FBI was suspicious that Lee passed classified data to China about America's neutron bomb. In that case, Lee had telephoned a fellow Taiwanese-born scientist at the Livermore lab near San Francisco in late 1982 and was overheard on an FBI wiretap. According to an American intelligence official, Lee's comments were "suspicious" but not conclusive. Consequently, the FBI administered a polygraph test to Lee in January 1984 as part of an investigation code-named Tiger Trap. The test sought to determine if he had contact with foreign intelligence services or had inappropriately shared classified information. Lee failed the test. His answers indicated deception on seven questions dealing with his contact with foreign intelligence services and whether he had inappropriately shared classified information.

Lee was given a chance to explain his answers to the FBI. He was retested and passed. The FBI then put a "cleared" notice on the final page of the 18 page polygraph report. The DOJ turned out the FBI's requests to obtain a wire tap on Lee's phone or a search warrant for his home.

In 1988, Congressional sources said that CIA agents were approached by a Chinese scientist who offered to spy for the United States. The scientist handed over a one page document suggesting that China had data on a highly advanced warhead design called the W-88, a miniaturized warhead originally developed at Los Alamos. Although the document did contain some classified data, it was primarily drawn up from declassified information and contained nothing proving that the Chinese actually acquired the W-88. The agents concluded the scientist was in fact a spy for the Chinese and rejected his offer. The Chinese had good reason to want the CIA to believe it had the W-88.

Nothing transpired for seven years. Then in 1995, Notra Trulock III, the DOE's director of intelligence, concluded that China had acquired critical information on the W-88 from the United States. Trulock's conclusion differed with that of the CIA which had found no such evidence. The same year, Lee attempted to delete files from his computer shortly before he was fired for security violations on March 8. The FBI believed that Lee's computer contained "dozens of non-classified codes" containing several hundred thousand lines of computer code.

In 1995 the CIA obtained a 1988 Chinese military document which described the weight, dimensions, explosive yield, and other significant details of six American nuclear warheads and the ballistic missiles that carry them. In addition hand-drawn sketches of the reentry vehicles that house the warheads were obtained by the CIA. However, officials said that the documents did not contain sufficient information for the Chinese government to copy or construct American-style nuclear weapons. American intelligence officials maintained that a chart in the Chinese-language document provides accurate data on America's W-56, W-67, W-72, W-78, W-87, and W-88 nuclear warheads. The first three warheads date back to the 1960s or 1970s, and were no longer deployed by the United States. However, the W-87, which sits on the MX "Peacekeeper" missile, and the Trident submarines' W-88, have been America's most sophisticated nuclear weapons. The W-78 is on Minuteman III missiles and is also considered highly accurate. The W-87 carries 10 independently targeted warheads inside its reentry vehicle, or nose cone. The W-88 has up to eight, and the W-78 has three. Together, the weapons are considered the backbone of America's nuclear arsenal.

In 1996, the DOJ denied an FBI request to examine Lee's office computer and warned that evidence obtained without proper permission would be inadmissible in court.

Trulock was the first to investigate Lee in the summer of 1996. Robert Vrooman, the former head of counterintelligence at the Los Alamos laboratory, and Charles Washington, the former acting head of intelligence at the Energy Department, both said that Trulock had acted out of a racist view that Lee was more inclined to spy for China because of his ancestry.

The first media story broke on March 6, 1998 when the New York Times headlines read , "China Stole Nuclear Secrets for Bombs, U.S. Aides Say." The story read in part that China had made "a leap in the development of nuclear weapons: the miniaturization of its bombs ... accelerated by the theft of American nuclear secrets from Los Alamos National Laboratory in New Mexico."

Lee was fired two months ago after failing another FBI polygraph test that focused, in part, on whether he had passed classified data on nuclear warheads while attending scientific conferences in Beijing in 1986 and 1988. DOE Secretary Bill Richardson ordered that Lee be fired from Los Alamos for failing to report contacts with officials from "sensitive" countries. Lee had not disclosed meeting with a Chinese scientist on his previous trip to China. Richardson also noted that Lee earlier had provided deceptive answers on a polygraph test regarding his possible mishandling of computer files. After Lee's dismissal, his house, office, and computer were all searched.

The FBI launched another probe into allegations that nuclear secrets had been passed on to China. Code-named Kindred Spirit and involving dozens of federal agents, the FBI's investigation confirmed that Chinese espionage of American nuclear warhead design secrets began in the 1980s and may have involved the compromise of highly classified computer programs and data from hundreds of underground nuclear tests and simulations.

Three weeks after Lee was fired, the FBI determined that Lee had used a large magnetic tape drive to improperly transfer nearly 2,000 classified computer files, containing computer programs and data derived from hundreds of underground nuclear weapon tests and simulations, into an internal lab computer network that is considered vulnerable to outsiders. Lee was not among those in the lab who was supposed to know how to transfer the files. He tried to delete the files from his computer two days after he failed the polygraph test but before he was fired. DOE officials said that the files were accessed at least once after they were moved, but it remains unclear whether anyone other than Lee was involved. The transfers began in 1983 and ended in 1995, when new lab computer regulations prevented such file transfers.

THE FBI'S ATTEMPTS TO SET UP LEE. In mid-1998, the FBI attempted to catch Lee in a "false flag" operation. Chinese-speaking FBI agents called Lee and tried to lure him to a meeting by pretending to be Chinese spies. He refused to go after the bait.

Then on March 7, 1999, Lee was interrogated by FBI agents the day before he was fired from his job at Los Alamos. According to the Washington Post (January 8, 2000), agents deliberately misled Lee into believing that he had failed a DOE polygraph test, as they pressed him to confess to passing nuclear weapons secrets to China. The interrogation came at a critical juncture in the FBI's attempt to determine how China might have obtained secrets about the design of the W-88 warhead. Throughout the interrogation, FBI agents pressed Lee to admit that he had passed secrets to Chinese scientists at his Beijing hotel in 1988. The agents suggested that unless he confessed, he would be arrested and possibly executed. One agent asked Lee, "Do you know who the Rosenbergs are? The Rosenbergs are the only people that never cooperated with the federal government in an espionage case. You know what happened to them? They electrocuted them, Wen Ho."

Lee insisted throughout the tape-recorded session that he was telling the truth, unaware that polygraph examiners actually had given him an extremely high score for honesty. Lee told the FBI agents, "I don't know why I fail. But I do know I have not done anything. ... I never give any classified information to Chinese people. I'm an honest person and I'm telling you all the truth, and you don't believe it."

The attempt by the FBI to coerce a confession from Lee demonstrated that the FBI was employing devious tactics. The polygraph examiners concluded that Lee was telling the truth when he said he had never passed classified information to China. But two months later, FBI polygraph examiners concluded that Lee was being deceptive when he was asked the same question.

CONGRESSIONAL INVESTIGATIONS LEAD TO A DEAD END. The first congressional probe into alleged mishandling of classified documents began with the Cox committee in the House. In 1998, the Cox committee, headed by the California Republican congressman, dug up evidence which indicated that Lee was a "chief suspect" of passing on classified information on the neutron bomb to the Chinese government. The Cox report was made public on May 24, 1999. It did not contain any evidence that Lee had committed a crime. In fact, the committee never mentioned Lee's name. Although the Cox report castigated the Clinton administration for failing to detect the passing of nuclear secrets at Los Alamos, the breach of national security began in the Carter administration and continued for 12 years in the Reagan-Bush years. But the real breach quite possibly came from the American corporations -- Hughes Electronics and Loral Space and Communications -- which dealt clandestinely for nearly a decade with the Chinese government.

Although not charged with a crime by the Justice Department, Lee's attorneys attempted to thwart an indictment. They filed a brief with the DOJ, arguing that Lee "used considerable care" to protect the security of secret nuclear codes when he transferred data to an unclassified computer system. According to the brief, Lee took care to safeguard data in his unclassified computer system by adding an extra level of password authority. An outsider would have had to break three password codes and then correctly guess the file name to gain access to any file. Lee's lawyers argued, equivalent to "a triple-bolted safe." Lee's attorneys maintained that the transfers were made for "a good reason." They argued that Lee was a victim of political hysteria and "a scapegoat for the scandalous lack of security" at Los Alamos.

The brief said that one reason Lee used the unclassified system was because of an incident in 1994 when a lab computer conversion project inadvertently erased "lines of code (Lee had) spent years developing." His attorneys claimed that the classified computer system could crash and wipe out other work made the transfer seem "a reasonable precaution" to Lee.

Lee's lawyers also contended that no American civilian had ever been criminally prosecuted for mishandling classified information, especially in the absence of evidence that it resulted in loss of that material. They also maintained that any prosecution of Lee would be the result of "xenophobia and political agendas" since Lee was of Chinese origin and born in Taiwan.

Lee was never charged with espionage. Even the New York Times, which was one of the leading newspapers to publish stories on Lee's alleged connections with China, concluded that Cox's congressional report "went beyond the evidence" to support its claims that the Chinese made a weapons breakthrough based on stolen American secrets. The Times said that there was inconclusive evidence to implicate Lee and that "the federal investigation focused too soon" on him. The Times said that "the lost secrets" had been available to "hundreds and perhaps thousands of individuals scattered throughout the nation's arms complex." Those secrets were also well known to Russia, France, and Britain who had been spending several years building the miniaturized nuclear warheads which China, too, presumably was attempting to develop.

Even though Cox emphasized that he did not single out Lee in his committee's investigation. But the reason why Lee's name was not used in the hearings was because he was still being investigated by the FBI. Lee was at the center of the charges Cox was pursuing. In fact, Trulock, who headed the original investigation in 1996, testified that Lee was responsible for the leaks to the Chinese government. But Trulock was not a weapons design scientist, Yet Cox and his colleagues were convinced by Trulock that Lee was responsible for passing on classified documents to Beijing.

Vrooman, the former head of counterintelligence at Los Alamos, testified that Lee's case was "built on thin air." Vrooman stated that there was not a "a shred of evidence" that linked Lee to the Chinese. Vrooman pointed out that a detailed description of the miniaturized W-88 warhead had been distributed to 548 addresses throughout the government, the National Guard, and private defense firms.

While the Cox committee conducted its investigation, the Senate Governmental Affairs Committee initiated its probe into alleged security breaches. This committee identified numerous flaws in the FBI's investigation, including the decision to target Lee as the only suspect.

While still investigating Lee, the FBI launched a probe of the Sandia and Lockheed labs -- not at Los Alamos -- where the W-88 was created. Not only did Lee have nothing to do with the sketch of the warhead, but the Associated Press reported that the FBI had known this fact for over a year. The existence of this exculpatory evidence regarding Lee was revealed in a letter to the Senate in November by Assistant FBI Director Neil Gallagher who heads up national security cases for the FBI. Gallagher wrote that the Albuquerque FBI office in charge of the investigation filed reports in November and December 1998 and again in January 1999 that "question the accuracy of certain representations and conclusions" about the original evidence against Lee. The Associated Press also reported access to a document from the FBI dated January 22, 1999, stating that "the FBI office in Albuquerque continues to insist" that Lee had nothing to do with the China spying case. FBI Director Freeh was briefed by agents in Albuquerque March 1999 and again said that "it did not appear" that Lee had anything to do with the theft of the warhead design.

Clinton's Foreign Intelligence Advisory Board met and publicly raised questions about the FBI's investigation of Lee. In June the board concluded that technical information about the W-88 "had been widely available within the U.S. nuclear weapons community," including the DOD, Energy Department, and numerous private contractors, as early as 1983. But only one investigation was initiated by the FBI and DOJ.

As a result of the mismanaged investigation by federal authorities, the Senate voted in September to approve a defense funding bill which included a plan to create a an agency within the Energy Department to run the nation's nuclear weapons complex. The reorganization plan created the National Nuclear Security Administration which established a chain of command, one where accountability would not be questioned and one where the line of authority led directly to the top. In September 1999 Reno and Freeh announced that they would start from the beginning and launch a new probe by investigating more than 500 potential suspects at nuclear power sites across the country.

Lee's lawyers sent letters to the Justice Department shortly before he was indicted, specifically offering to let him take a polygraph test to answer questions about the tapes. The offer was ignored. But the Energy Department soon decided to play hardball. On August 12, 1999, after Vrooman had retired from Los Alamos, Richardson issued reprimands to Vrooman and two colleagues at the lab for allegedly failing to assist the FBI in its pursuit of Chinese espionage. Vrooman was barred from being a consultant for the department for five years. Another counterintelligence official at the lab, who also was disciplined, quit.

Angry at what he viewed as a cover-up, Vrooman went public. His complaints about racial profiling and what he called a complete lack of evidence against Lee were the first indications that the case was seriously amiss.

THE GAO INVESTIGATION. In January 1999, a senior FBI official misled Congress about the uinvestigation. FBI Assistant Director Neil Gallagher told a Senate committee in June 1999 that he had "full confidence" in the initial investigation by the Department of Energy. But in a report sent Thursday to Congress, the GAO said Gallagher "had ample opportunity to know and should have known" about an FBI memo expressing "serious concerns" about the investigation. (Los Angeles Times, June 29, 2001)

That document was sent from the FBI's Albuquerque field office to headquarters on January 22, 1999 -- more than a month before Lee was fired from Los Alamos. The GAO's Office of Special Investigations said it was unable to determine whether Gallagher, who headed the FBI's National Security Division, intentionally misled the committee. (Los Angeles Times, June 29, 2001)

The report said, "Mr. Gallagher told us that he did not lie or purposely mislead the Congress, but that he inadvertently gave incomplete testimony." GAO investigators determined that a copy of the January 22 memo was included in a briefing book prepared for Gallagher prior to his Congressional testimony. The GAO report said that Gallagher acknowledged failing "to read the briefing book in its entirety." GAO investigators also reviewed a February 22 memo from Gallagher to the Justice Department in which he forwarded various documents in the Lee case, including the January 22 Albuquerque memo. Gallagher said in his rebuttal that the February 22 memo was written and initialed on his behalf by a subordinate. (Los Angeles Times, June 29, 2001)

According to the GAO report, Gallagher told GAO investigators that he first learned of the January 22 memo after his Senate testimony during a conversation in late June or early July 1999 with the agent in charge of the FBI's Albuquerque office. In his rebuttal, Gallagher said it was worth noting that the special agent also told GAO investigators that "it was clear to him that I was unaware of the January 22, 1999, document that he was talking about." (Los Angeles Times, June 29, 2001)

A NEW INVESTIGATION OF LEE. The FBI was stalled, unable to prove that Lee had passed on classified documents to China. Lee was never found in possession of the secret sketch of the W-88 nuclear warhead. In fact he never had access to the sketch. The Justice Department conceded in December that Lee and the Los Alamos lab never had access to the flawed design drawing of the weapon. Unable to link Lee with passing secrets to Beijing, the agency began its investigation all over in September. Three months later Lee was arrested on 59 unrelated counts of mishandling secret nuclear weapons computer programs and data at Los Alamos. At Lee's arraignment hearing in a Albuquerque federal court, prosecutors alleged for the first time that Lee stole computerized nuclear weapons development, testing and design secrets "sufficient to build a functional thermonuclear weapon."

Four years after the FBI had begun its investigation, a federal grand jury in New Mexico indicted Lee. He was charged with 59 counts of illegally removing highly classified design, construction, and testing data. The indictment charged that Lee had violated the Atomic Energy Act and Foreign Espionage Act, assembling collections of 19 computer files that contained nuclear weapons secrets; transferring classified information into unclassified computer files at the Los Alamos laboratory and downloading other material onto portable tapes; and mishandling nuclear data. The indictment said that seven of the tapes that Lee had made, containing critical nuclear secrets, could not be found.

Lee was charged under two sections of the United States Code. First, Title 42, Section 2275: Receipt of Restricted Data. Whoever, with intent to injure the United States or with intent to secure an advantage to any foreign nation, acquires, or attempts or conspires to acquire any document, writing, sketch, photograph, plan, model, instrument, appliance, note, or information involving or incorporating restricted data shall, upon conviction thereof, be punished by imprisonment for life, or by imprisonment for any term of years or a fine of not more than $20,000 or both.

Second, Section 2276. Tampering, Altering, Concealing and Removing Restricted Data Whoever, with intent to injure the United States or with intent to secure an advantage to any foreign nation, removes, conceals, tampers with, alters, mutilates, or destroys any document, writing, sketch, photograph, plan, model, instrument, appliance, or note involving or incorporating restricted data and used by any individual or person in connection with the production of special nuclear material, or research or development relating to atomic energy, conducted by the United States, or financed in whole or in part by federal funds, or conducted with the aid of special nuclear material, shall be punished by imprisonment for life, or by imprisonment for any term of years or a fine of not more than $20,000 or both.

The FBI claimed that it obtained evidence in Lee's house during its April 10 search, indicating that Lee had attempted to mislead one of his colleagues, allowing him to use his insecure office computer to download classified documents. The FBI spokesman said that the agency uncovered a record maintained by Lee in Chinese. Lee convinced his co-worker as early as 1993 that he was working on a personal resume. Lee then placed the classified material pertaining to nuclear weapons on magnetic tapes during the middle of the night and on weekends. According to the FBI, Lee had to certify to the computer that he was transferring unclassified materials. Four years later in 1997, the FBI asserted that Lee downloaded "Tape N," containing the most current information on nuclear weapons, from a classified computer and that he placed the data on an unclassified computer.

Prosecutors at the arraignment said that Lee had taken all of the Los Alamos files which related to nuclear weapons development over the last 50 years. If convicted of the most serious offenses in the indictment, removing classified nuclear weapons data, Lee could face a life sentence in prison.

Prosecutors also claimed that Lee spent more than 40 hours moving the files on nights and weekends in 1993 and 1994 and repeatedly deceived his colleagues about his intentions. Robert Messemer, the FBI agent in charge of the case, testified that Lee effectively had declassified the equivalent of more than 400,000 printed pages of highly classified computer data. Messemer also testified that the FBI found a notebook on April 10 while searching his house. Written in Chinese, it listed all the classified and unclassified files that Lee had moved. The notebook also indicated that Lee had put the data on at least 15 high-density portable data tapes. Six were later located in Lee's office, and two others were determined to contain unclassified data. The FBI maintained that Lee transferred the files in order to protect the data in case the main Los Alamos computer crashed, as well as to make his work easier.

The Los Angeles Times (March 7, 2000) reported that when Lee was fired in March 1999, the FBI doubted that he was involved in espionage. While the Senate was considering legislation to prevent classified leaks in the future, GOP Senator Arlen Specter said that FBI investigators were "thrown off" course in early 1999 after they were informed by the DOE that Lee had passed a polygraph examination in December 1998. Specter maintained that subsequent FBI reviews showed that he failed the test. However, Mark Holscher, Lee's lawyer, disputed Specter's contention that Lee failed the DOE polygraph, saying three DOE polygraphers had given Lee high passing scores.

In January 2000, federal prosecutors convinced District Judge James A. Parker in New Mexico that Lee was such a clear threat to national security that he should be jailed without bail. Lee was confined to a small cell and was not allowed to see visitors. While Lee awaited his November trial eleven months down the road, defense lawyers argued that several discrepancies had occurred during Lee's incarceration over a period of one year. Attorneys maintained that crucial parts of the government evidence against Lee were false or misleading. They continued to maintain that he was unjustifiably denied bail. And they showed that he actually had passed a polygraph test.

But Trulock continued to insist that a Chinese spy had looted Los Alamos and that Lee was the only suspect. Trulock found powerful allies among Republican congressman who were urged to use the Lee case to criticize the Clinton administration for lax security in the face of wholesale nuclear theft. Trulock had little respect from his colleagues, according to the Los Angeles Times (September 13, 2000). One of them, Charles E. Washington, who worked for Trulock as acting director of counterintelligence, said in a sworn affidavit filed on Lee's behalf that Trulock "acts vindictively and opportunistically, that he improperly uses security issues to punish and discredit others and that he has racist views toward minority groups." In a telephone interview with the Los Angeles Times, Washington said that he once was forced to call outside police to the Energy Department headquarters "due to Mr. Trulock's abusive behavior" during an argument. "He spat on me," he added.

Trulock became the subject of an investigation of whether he disclosed secrets in an unpublished article about the investigation, according to the New York Times (September 11, 2000). He claimed that the FBI bungled the investigation. FBI spokesman Steven Berry had no comment. At that time, Trulock had developed a list of 70 people at Los Alamos who had visited China at some point. That initial list of suspects was then narrowed to 12. Trulock said that the list was given to the FBI which rejected the other 11 suspects, including Lee's wife, Sylvia, who also worked at the laboratory, and focused on Lee. The list of 70 included people with no access to classified or weapons information and whose trips to China had no relationship to their work at the laboratory. One woman, for instance, who had no access to secrets, went to China with a high school band. Another person with no access to secrets went to China to participate in joint meteorological experiments. But an Anglo scientist involved in hydrodynamics, Lee's specialty, was involved in classified weapons work and went to China for a professional visit. Yet he was not included on the list of 12.

According to the Los Angeles Times, the FBI said that it generated its list of suspects using a "matrix," a set of criteria it could compare with a long list of suspects. Trulock insisted that the matrix was fabricated several years later as a ploy to persuade the Justice Department to provide a warrant to tap Lee's phones. That effort failed in 1997. Trulock wrote a letter to Congressman Porter Goss, Republican of Florida, the chairman of the Select Committee on Intelligence, on July 24, 2000. He stated, "At no time was a matrix developed and the final DOE report to the FBI contains no mention of a matrix."

Vrooman said that he investigated Lee a number of times and became convinced that, while he may have been naïve, he was not a spy. Nevertheless, he complained that while Lee did meet some of the criteria investigators were looking for many others who also did were left off the list of 12 suspects. Vrooman said that 15 people who did nuclear weapons research and visited China had been omitted from the list.

As a result of the witch-hunt, several careers were ruined. Robert Messemer, the FBI's chief investigator in the Lee case and a specialist in Chinese counterintelligence, was the government's key witness against Lee -- but instead he turned into their weakest link. During a mid-August bail hearing for Lee, Messemer admitted from the stand that his previous testimony was wrong when he said repeatedly that Lee had lied and sought to hide his actions when he copied the weapon files and created the tapes. One of Lee's colleagues had told the FBI that Lee had asked for password access to his computer to download some files or data. Messemer interviewed the scientist, Kuok-Mee Ling, at least six times and reviewed transcripts of his other statements. Messemer nonetheless had testified falsely to two judges on three occasions that Lee had lied to Ling by saying that he wanted to download a resume. Messemer also acknowledged that, despite his testimony earlier in December and despite a prosecution document filed with the court in June, the FBI had no evidence to show that Lee had applied for jobs at six academic or nuclear institutes overseas. Prosecutors had argued that Lee might have created the tapes to enhance his job prospects. As a result, the government had no solid evidence against Lee.

LEE APPEALS. In Lee's first appeal for bail, he was rejected by a magistrate and then by Judge Parker. And an appeals court rubber-stamped the judge's decision. In the mean time, Lee's family and friends offered a $2 million property bond to obtain his release. They said that more than a dozen homes and businesses would be forfeited to the federal government if Lee jumped bail. Lee's supporters, largely in the Asian-American community, raised more than $400,000 for his defense, and most of his defense lawyers did their work on a pro bono basis or at a heavily discounted rate.

During his incarceration in 2000, Lee continued to drum up support from a growing number of scientific, academic, civil rights and Asian American groups. More than 1,400 scientists signed a petition, for example, protesting the treatment that Lee faced since while he was jailed. The petition was circulated by the New York Academy of Sciences, the Committee of Concerned Scientists, the American Association for the Advancement of Science, and the American Physical Society.

Lee made his third bid for bail in August when he appeared for a pretrial hearing before District Court Judge James Parker. The judge ruled that the government needed to find a way to describe in open court the nuclear secrets he was accused of copying. But Parker also said that Lee's defense team had to show that he knew that at least some of the information he downloaded from the classified computer system had already been published.

Lee's lawyers called on John Richter, a former senior weapons designer and intelligence official at Los Alamos, to testify. As reported in the Los Angeles Times (August 19, 2000), he told Parker that perhaps 99 percent of the information Lee allegedly copied already was available in open literature and that it would not be useful to a foreign country. Additionally, Richter flatly denied that the material "represents a complete nuclear design capability," as government witnesses previously had claimed. And, asked whether national security would be at risk if a hostile power obtained the data, Richter replied, "I don't think that it would have any deleterious effect at all."

Lee's lawyers submitted affidavits before the hearing from two other senior Los Alamos officials that raised similar questions. Harold Agnew, a former director of the lab, and Walter Goad, a Los Alamos weapons expert, both said that the downloaded information was publicly available in various forms and that the government's presentation in December 1999 was aimed at intimidating Judge Parker.

Lee's lawyers also pointed out that FBI lead investigator Robert Messemer, the prosecution's lead witness, conceded that he "inadvertently" misled Judge Parker during the December 1999 hearing. Parker repeatedly cited Messemer's testimony in his ruling denying Lee bail. Messemer testified at the time that Lee had lied to a colleague by asking for password access to his computer to download a resume. But Messemer conceded that the scientist, Kuok-Mee Ling, repeatedly told the FBI that Lee had asked to download data files, not a resume. Messemer apologized to Parker, "At no time did I intentionally provide false testimony. I made a simple, inadvertent error."

But Lee's lawyers argued that Messemer misrepresented facts two other times during his testimony. Although Messemer had said that Lee had not disclosed a meeting with Chinese scientists during a lab-approved visit to Beijing in 1986, Lee's lawyers produced a document showing that Lee had reported the meeting after his return to Los Alamos. Messemer said that he had not read the report before he testified. He also acknowledged that the FBI had not questioned Lee about the contacts at the time. Messemer also testified in December 1999 that the FBI had found letters during a search of Lee's home, indicating that he had applied for jobs at six overseas institutes. But prosecutors later asserted that Lee may have copied the weapons secrets in an attempt to enhance his job prospects. Messemer said told Parker that the FBI had no evidence that the letters were ever mailed and that none of the institutes contacted by the FBI had a record of receiving them.

Misleading information about Lee's polygraph results again resurfaced. Messemer told Parker that Lee passed a 1999 polygraph exam administered by the Wackenhut Corporation security company, according to the Associated Press. But after Lee was fired from Los Alamos in March 1999, Energy Secretary Bill Richardson said that Lee had failed a polygraph test. Under questioning by defense lawyer Mark Holscher, Messemer said he was aware that Lee had scored among the highest possible scores for credibility on the test when Lee denied passing secrets, denied contacting anyone for the purpose of espionage, and denied intending to harm the United States.

Messemer also testified that during an FBI interrogation on March 7, 1999, agents warned Lee that he might be given the death penalty for stealing nuclear secrets. They repeatedly compared his case to executed Soviet spies Julius and Ethel Rosenberg. Until that interview, Messemer said, Lee had voluntarily submitted to 20 meetings with FBI agents without a lawyer. He since declined to meet with the FBI.

LEE'S PLEA BARGAINAfter three days of the pretrial hearing, Parker ordered Lee's release on $1 million bail week. This ended a nine month incarceration in solitary confinement where Lee was barred from receiving visitors and telephone calls in his tiny cell. He was placed under house arrest at his home in White Rock, New Mexico where he prepared for his trial in November. In granting bail, Parker did not specifically address the merits of the charges against Lee. But he reached his decision even before reviewing all of the material supplied during a three day pretrial hearing. Quoted in the New York Times (August 25, 2000), Parker said, "Enough of the transcript of the most recent hearing has been prepared and reviewed by me to permit the announcement of a ruling at this time. I conclude that there now is a combination of conditions that will reasonably assure the appearance of Dr. Lee as required and the safety of the community and the nation."

The American Civil Liberties Union, Asian American groups, and other scientific organizations voiced complaints since Lee was jailed under unusually harsh conditions in December. Then on August 31, in an unprecedented move, the three most prestigious scientific academies in the United States publicly protested the government's incarceration of Lee. They released a statement, complaining that Lee appeared to be a victim of unjust treatment and that his case reflected poorly on the American justice system. The letter was sent by the presidents of the National Academy of Sciences, the National Academy of Engineering, and the Institute of Medicine to Attorney General Reno.

In their letter, the presidents of the academies did not claim that Lee was innocent. According to the New York Times (September 1, 2000), they argued that "inaccurate and detrimental testimony by government officials resulted in Dr. Lee needlessly spending eight months in prison under harsh and questionable conditions of confinement. ... We also urge that those responsible for any injustice that he has suffered be held accountable. Even more importantly, perhaps, we urge that safeguards be put in place to ensure that, in future, others do not suffer the same plight." The two-page letter was signed by Bruce Alberts, president of the National Academy of Sciences, William Wulf, president of the National Academy of Engineering, and Kenneth I. Shine, president of the Institute of Medicine.

Judge Parker ordered the scientist's release and issued a statement which said that he was no longer convinced that Lee had downloaded some of the country's most sensitive nuclear secrets. Quoted in the Los Angeles Times (September 5, 2000), Judge Parker wrote, "What the government described in December 1999 as the ‘crown jewels' of the United States nuclear weapons program no longer is so clearly deserving of that label."

Judge Parker was even more critical of the prosecution, saying that it "failed, at this time, to meet its burden." He said that he remained "seriously concerned" about some of Lee's actions, such as failing to tell Los Alamos officials that senior Chinese weapon scientists hoped to obtain classified information during a secret meeting in Lee's Beijing hotel room in 1988. However, the judge pointed to testimony from an FBI agent who acknowledged that several pieces of key testimony he gave during Lee's first bail hearing were incorrect. Judge Parker also said that the conditions he required for Lee's release would strictly limit his movements and would prevent him from passing on several of the computer tapes the government says were missing.

However, on September 1, a federal appeals court blocked Judge Parker's decision and issued an emergency to delay Lee's release on $1 million bail. The 10th Circuit Court of Appeals in Denver ordered the stay before the United States attorney filed a formal appeal to prevent Lee from going home.

But nine days later, the case against Lee came to an abrupt end when the government agreed to drop virtually its entire case against him. In return, Lee agreed to plead guilty to a single charge that he improperly downloaded classified material onto an unsecured computer. Lee pled guilty to one felony count, the 57th of the original 59 count indictment, in which he admitted to improperly gathering and retaining national security data. The other counts, which could have brought him a life sentence, were dropped. The sentence given Lee was time- served -- nine months.

The plea agreement was worked out after the government suffered a string of courtroom defeats; after an FBI agent recanted testimony in which he had said that Lee had engaged in deceptive behavior; and as the government faced a deadline to hand over thousands of pages of classified documents about why it singled out Lee after an investigation that went back to 1995.

Prosecutors said that they were satisfied by the plea bargain, presumably since it turned into a highly embarrassing case. They said that they were motivated to accept the agreement because they feared that Judge Parker would have forced the government to disclose in open court highly classified information about the country's nuclear weapons program. Officials claimed that the plea bargain negotiations began before the judge ordered Lee released on bail.

According to the New York Times (September 11, 2000), one government official said, "We got a felony conviction. He's admitted to what he said he didn't do. Finding out what happened to the tapes was a lot more important than putting a 60-year-old man in prison for the rest of his life." Lee's lawyers had always said that he had destroyed the seven missing tapes.

But Lee was unable to walk free immediately. A last minute dispute between the government and defense lawyers over the plea agreement delayed his release. Finally, he was released two days later.

Earlier, Lee had filed a civil suit against the government, charging that the Energy Department violated his rights to privacy by publicly releasing incriminating evidence against him in an early stage of the investigation, such as details about his employment and travel and the results of a polygraph test. With the criminal case against Lee over, the civil litigation against the federal government could proceed.

Judge Parker harshly criticized the Justice Department for its tactics in the case and apologized personally to Lee. But Reno expressed no regrets over the government's tactics even though Judge Parker said that Lee deserved an apology for harsh treatment that had "embarrassed this entire nation." The attorney general said in the New York Times (September 13, 2000), "I think Dr. Lee had the opportunity from the beginning to resolve this matter and he chose not to and I think he must look to himself." In a meeting with reporters, Reno said she wished that Lee had agreed earlier to provide investigators with information about seven missing computer tapes onto which he transferred nuclear secrets.

In a stinging rebuke of the DOJ and FBI, Clinton expressed his concerns about the government's actions in the case, according to the New York Times (September 15, 2000). In comments to reporters, Clinton said he had long questioned whether prosecutors had adequate grounds to keep Lee in jail for nine months awaiting trial. The president said, "I always had reservations about the claims that were being made denying him bail. So the whole thing was quite troubling to me and I think it's very difficult to reconcile the two positions that one day he's a terrible risk to the national security and the next day they're making a plea agreement for an offense far more modest than what had been alleged. I don't think you can justify in retrospect keeping a person in jail without bail when you're prepared to make that kind of agreement It just can't be justified, and so I, too, am quite troubled by it."

Justice Department officials castigated Judge Parker after he severely rebuked the government's handling of the case. James Robinson, head of the Justice Department's criminal division, said that the judge's criticism was misguided. According to the Washington Post (September 28, 2000), Norman Bay, the United States attorney for New Mexico, said that Judge Parker was unaware of plea negotiations in which Lee's lawyers had threatened to introduce American nuclear secrets in the courtroom, a tactic known as "graymail."

Bay told a Senate Judiciary Committee task force, "I've got great respect for Judge Parker, but don't know if he was aware of all of the discussions that had occurred between the parties. When we were sitting in the courtroom at sentencing, his comments came as a complete surprise to us. ... To be honest with you, I was very much blindsided by the judge's comments."

As part of the plea bargaining agreement in December, Lee told the FBI during 10 days of closed-door questioning under oath that he was a paid consultant in the late 1980s and early 1990s to a Taiwanese businessman. Lee testified that the businessman later helped arrange for him to spend four weeks at Taiwan's leading military research center, according to the San Francisco Chronicle (December 24 and 28, 2000). That same businessman also paid for Lee's air travel to Taiwan in December 1998, when Lee made a second, shorter visit to the military research center, the Chung Shan Institute of Science and Technology, the sources said.

Chung Shan allegedly was involved in past efforts by Taiwan to develop nuclear weapons. Lee told investigators that while at Chung Shan for four weeks in April and May 1998, he gave talks and "consulted on matters related to unclassified computer codes" for which he received "a modest fee of less than $5,000," according to the Chronicle. But he failed to report the payment from Chung Shan to officials at Los Alamos National Laboratory in 1998, as lab rules required, according to government sources.

THE INVESTIGATION OF THE JUSTICE DEPARTMENT. The final version of an Energy Department review concluded that Lee, who had visited China, was "the only individual identified during this inquiry who had the opportunity, motivation, and legitimate access" to pass the nuclear technology along to the Chinese.

The Bellows report, which was released by the Justice Department, found that one of the early and critical missteps in the Lee case came in 1995, after an Energy Department working group examined how the Chinese had gained sensitive W-88 nuclear warhead technology. While the working group identified a range of options, its findings were mischaracterized in follow-up reports and were never passed on to the FBI as it began examining possible suspects, the report said.

In August 2001, another investigation by the Justice Department concluded that it had "investigated the wrong crime" for nearly three years. Furthermore, the report said that the DOJ had been too aggressive on Lee as the prime suspect. Investigators ignored evidence that might have led them in other directions, mischaracterized their findings, and relied on scientific analysts with suspect credentials. The startling collection of blunders meant that investigators may never know how -- or even whether -- the Chinese government stole technology on the design of American nuclear warheads.

Even though it was the most critical report, it still rejected one of the central claims from Lee's supporters -- that he was unfairly branded a spy because he was Asian- American. Assistant United States Attorney Randy Bellows, who wrote the report last year at the request of then-Attorney. General Janet Reno, said that there was "no evidence of racial bias" in the investigation. He said that the plan to "identify" Chinese-Americans was never carried out. Moreover, the memo "was simply acknowledging the fact that (China) specifically targeted ethnic Chinese for espionage purposes," a viewpoint backed up by veteran counterintelligence agents.

The report suggested that investigators ignored a range of other possibilities, including that the Chinese developed the technology on their own or that defense contractors or Energy Department employees outside the Los Alamos lab were responsible for the breach. By mischaracterizing what it had found, the Energy Department "compromised and undermined the FBI's own investigative efforts. This is not to say that Wen Ho Lee did not warrant investigation. ... He did. Rather, it is to say that the mischaracterization of the (foundation of the Energy Department review) caused the FBI to ignore and exclude numerous other possible subjects and numerous other possible venues" for leaks. Investigators failed to search numerous laboratory vaults containing hundreds of thousands of pages of potentially useful documents, the report found. They relied on analysts whom they thought to be "scientific experts" but who in fact lacked fundamental knowledge about nuclear warheads. And they suffered a "terrible misunderstanding" during one interview that led them to erroneously exclude an entire lab, apparently Lawrence Livermore, from suspicion as a possible source of the technology breach.

Finally, the report said that the Energy Department investigators did not begin their initial probe looking to prove that Lee was a spy, but that suspicion became a "self- fulfilling prophecy. Given the review's) slap-dash quality, its flawed rationales, its complete mischaracterization of the predicate, and its queer mash of intense review of some pertinent records and complete ignorance of other venues of (security) compromise, once Wen Ho Lee was ‘tagged' with the patina of suspicion, the (review) was all but over. He would be ‘it.' " .. Had either the FBI or DOE done what it should have done, the FBI could have been investigating in the year 1996 what it is now investigating in the year 2000." (Los Angeles Times, August 14, 2001)

REVAMPING FBI PROCEDURES. As a result of the botched Lee case, the Justice Department revamped its procedures on national security investigations. In previous cases, the FBI was too slow to inform prosecutors about intelligence probes. Seeking to plug holes in existing policy, Deputy Attorney General Larry Thompson informed the FBI that he considered it "mandatory" for the bureau to notify criminal prosecutors when they found any evidence of criminal activity in national security investigations.

In addition, the General Accounting Office identified "serious problems" in the disclosure and coordination of such information, hindering the potential prosecution of spies, terrorists, and others who threatened national security. The findings reflected an on-going feud between FBI investigators and Justice Department lawyers over their priorities in national security cases. The primary mission of intelligence agents examining terrorist and espionage threats was to protect national security and avoiding disaster. But prosecutors wanted to ensure that there was enough usable evidence collected in the course of these investigations to convict the wrongdoers.

The report by the GAO cited poor coordination in two high-profile investigations: the FBI's investigation of the Lee case and its probe into allegations that the Chinese sought to buy influence in the 1996 presidential election by bankrolling illegal campaign contributions. While the GAO report did not discuss specific lapses in these two cases, it found that the FBI did not adequately keep prosecutors at the Justice Department informed about undercover operations, interviews, or even the existence of such national security cases. The report concluded that reforms instituted by Attorney General Reno in 1995 to improve coordination had actually made things worse.

The FBI, working with Justice Department lawyers outside the criminal division, had been reluctant to turn over intelligence information to prosecutors for fear that the courts would find such coordination to be improper under a 1978 law restricting the way foreign intelligence investigations can be conducted, the report concludes. The result, the GAO said, was an "overly cautious" reading of the law. (New York Times, August 16, 2001)