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Spies, Lies & Portable Tapes

The spy next door? Wen Ho Lee heading into court last December.

The days tick by slowly for Wen Ho Lee, the scientist who has been accused of downloading and transferring onto portable tapes virtually every nuclear-weapon secret in the United States arsenal. In late February, the Tenth Circuit Court of Appeals in Denver agreed with a federal judge in New Mexico that Lee is so dangerous he should not be allowed out on bail. The decision means he could remain incarcerated in a Santa Fe jail until he goes to trial this fall.

In the meantime, the harsh security measures that were implemented during his first few months in custody have eased up a bit. He has access to books and newspapers and magazines but remains isolated. He eats his meals alone in his cell and is kept away from other inmates when he is taken to the shower or escorted outside for an hour's worth of exercise each day. Initially he was prohibited from talking with his wife, Sylvia, in Mandarin Chinese, his native language, but now when she visits, an FBI agent who is also fluent in Mandarin Chinese is brought in to monitor their conversation. The FBI also monitors and records telephone calls from his two grown children.

The security precautions are necessary, federal authorities say, because Dr. Lee has access to information so valuable that a hostile nation could conceivably plan a Ninja-style commando raid and airlift him out of the country. But the image of this diminutive, grandfatherly scientist sitting in a gloomy jail cell has galvanized the international scientific community and led several organizations to write Attorney General Janet Reno protesting the harsh conditions of his incarceration.

Last spring, soon after Lee was fired from his job as a nuclear-weapons physicist at Los Alamos National Laboratory, authorities searched his computer and made a startling discovery: Lee had transferred from Los Alamos's classified computer network all the information needed to build a variety of modern thermonuclear weapons. The classified data, which is equivalent to 803 megabytes, or some 400,000 pages, was transferred to ten portable tapes. According to the government, seven of the classified tapes, as well as two additional tapes that contain unclassified but related information, remain unaccounted for. Speaking through his attorneys, Lee has said that he destroyed the tapes when he was fired, but the FBI believes he may still have them stashed away. So in the past year, the agency has conducted a massive worldwide search. In New Mexico alone, every storage locker and safe deposit box has been checked.

The search is unprecedented, but if the tapes were to fall into the wrong hands, several leading scientists have testified, it could upset the "global strategic balance" and lead to nothing less than the defeat of America's armed forces. What's even more astonishing is that all of the information that Lee downloaded onto the tapes was sitting on Los Alamos's open and unclassified network for five to six years, vulnerable to the most unsophisticated hacker. Authorities say they have no evidence that anyone swiped the secret information off the lab's unprotected network, but they also admit they have no proof that it hasn't been taken, either. This ambiguity, several officials in the weapons complex suggest, could have enormous consequences for the United States and its defensive strategies.

During two bail hearings held in Albuquerque last December, Lee's defense team tried vigorously to get the scientist released on bail. They pointed out that Lee had voluntarily surrendered his passport and was willing to subject himself to 24-hour electronic surveillance and sign an irrevocable waiver of extradition under which he would surrender his right to contest his return to the U.S. if he should be found in another country. But the FBI insists that Lee could communicate the whereabouts of the tapes to a foreign agent by just a few words, even a coded message hidden in such simple phrases as "Uncle Wen says hello" or "How is the weather today?" or "The fish are biting."

Lee's criminal defense attorneys, Mark Holscher in Los Angeles and John Cline and Nancy Hollander in Albuquerque, have ridiculed the cloak-and-dagger arguments. But a federal magistrate and a federal judge in New Mexico agreed with prosecutors that Lee does indeed appear to present an enormous threat to the entire nation. "The danger is presented primarily by the seven missing tapes, the lack of an explanation by Dr. Lee or his counsel regarding how, when, where and under what circumstances they were destroyed, and the potentially catastrophic harm that could result from Dr. Lee being able, while on pretrial release, to communicate with unauthorized persons about the location of the tapes or their contents if they are already possessed by others," U.S. District Judge James Parker wrote.

After Parker issued his ruling, Lee's lawyers appealed the case to the U.S. Court of Appeals. In late February, after wading through mounds of evidence and two transcripts of the bail hearings, the appeals court upheld the earlier rulings. The release of Dr. Lee, the court concurred, could jeopardize not only the immediate community but also the United States as a whole. "We can conceive of few greater threats to the safety of the community than the risks presented in this case," the three judges wrote, the gravity of the situation seeping into their normally dry language.

But who is Wen Ho Lee? And how did Lee, who once hoped to open a Chinese restaurant after he retired from the business of making weapons of mass destruction, become such a threat to the entire nation -- indeed, the entire planet, as some of his former colleagues allege? Some of the answers can be found in the documents and hearing transcripts that were submitted earlier this year to the Denver-based appeals court. But the biggest question of all, the question that gives this case its highly charged drama and draws reporters from around the world, is whether Lee was really a spy: Did he pass, or did he intend to pass, America's nuclear secrets to a foreign government? Judging from the evidence submitted thus far, that question may never be answered.


Wen Ho Lee was born in Nantou, Taiwan, in 1939, just months after two scientists in Nazi Germany inadvertently split the uranium atom, a discovery that set off a frenzy of scientific research and culminated in the creation of the world's first atomic bombs. He was born into a large extended family and has two brothers and a sister living in Los Angeles and three sisters living in Taiwan. "He is a really simple man. His family were farmers," says Cecilia Chang, whose family has known the Lees for twenty years and is spearheading his legal defense fund from Fremont, California.

Lee attended Keelung High School and later went on to Cheng Kung University in Taiwan, where he obtained a bachelor's degree in mechanical engineering in 1963. According to a brief biography attached to his doctoral dissertation, at some point he also served in the Taiwanese air force.

After graduating college, Lee entered the United States and enrolled in the mechanical engineering program at Texas A&M University. He got his master's degree in 1966 and his Ph.D. in mechanical engineering in 1969. "He seemed to be a nice, quiet individual," recalls Fred Kettleborough, who chaired Wen Ho Lee's thesis committee. Kettleborough remembers little more about Lee; his dissertation, he says, seemed "average." Titled "Laminar Convection Between Two Vertical Plates," the paper is the study of how heat travels between two parallel surfaces. It was a precursor of what would become Lee's focus as a hydrodynamicist: the study of shock waves produced by nuclear detonations.

Lee became a naturalized U.S. citizen in 1974, and by the end of the decade, he was working at Los Alamos National Laboratory. Situated atop an arid mesa in northern New Mexico, Los Alamos has been the center of this country's nuclear-weapons research for more than fifty years. The lab has designed about 85 percent of all the weapons in the current stockpile, including the two atomic bombs that were dropped on Nagasaki and Hiroshima in 1945.

Spy scandals have periodically disrupted the tranquil calm of the small, conservative community. Klaus Fuchs, a quiet bachelor who babysat for many prominent scientists on the Manhattan Project, the wartime effort to build an atomic bomb, passed many of the bomb's secrets along to the Soviet Union, a clandestine effort that helped the Soviets detonate their first atomic weapon by 1949. And in 1953, Julius and Ethel Rosenberg were executed at Sing Sing for giving the Soviets top-secret nuclear-weapons data that they had obtained from Ethel's brother, David Greenglass, a Los Alamos employee.

In 1981, Dr. Lee went to work in the lab's top-secret X Division, where the actual design and research on nuclear weapons is done. With supercomputers capable of crunching billions of bits of data per second, the scientists in X Division use complex mathematical formulas to model what happens when atomic and hydrogen bombs are exploded. Wen Ho Lee, like the 350 other scientists working in the division, had a "Q clearance," which gave him access to all levels of classified and unclassified data, including information that was labeled top secret.

For decades, X Division's activities had been shielded from all but a select group of people. But during the two bail hearings last December, the esoteric art of designing nuclear weapons was laid out for the world to see. Since 1992, when President George Bush signed an executive order that put an end to actual testing, weapons scientists have been forced to rely on computer simulations and laboratory experiments. As a result, the major tools for designing nuclear weapons are source codes, sets of instructions given to a computer to simulate the seconds leading up to the fiery birth of a nuclear explosion and the enormous heat, radiation and shock waves released afterward. Written in computer language that can also be read by humans, the source codes are hundreds of thousands of lines long, or the equivalent of a very thick book. They contain everything that has been learned about atomic and hydrogen bombs from the actual explosions. The source codes, says Stephen Younger, a Los Alamos physicist who oversees some 3,500 people, are "among the most complex computer simulation tools ever developed on the planet."

When a nuclear detonation is simulated, these source codes, as well as vast amounts of related data, are fed into the computer. Input decks, which are essentially electronic blueprints, tell the computer about the geometry and materials of the weapon to be simulated. Data files contain supplementary information about the physical and radioactive properties of materials and how they will behave under pressures and temperatures that mimic those found inside our sun.

Within X Division, there were many subspecialties among scientists. Some worked on "primary codes," others on "secondary codes." A modern thermonuclear weapon, which is capable of killing several million people at one time, consists of a primary and a secondary stage. In simplest terms, the primary is a core of plutonium surrounded by a wrapping of high explosives; when imploded, the plutonium begins to fission, releasing X rays that compress the nearby secondary and ignite the enormously more powerful (and militarily significant) fusion processes. There were code physicists, such as Wen Ho Lee, who actually wrote the complex formulas that went into the source codes, and design physicists, who used the codes to design the weapons. Because the source codes were so lengthy, scientists generally specialized on one piece of the code. (It might take one of Los Alamos's Cray supercomputers twelve hours just to run a simulation of a secondary stage.)

During his tenure at Los Alamos, Dr. Lee worked on several codes. "He was the person who would put in new models, debug existing models for hydrodynamic flow," Richard Krajcik, a respected physicist and deputy division director of X Division, testified at one of the bail hearings. "His job was to assure that the hydrodynamics and the materials and physics functions of the codes that he worked on were working properly."

Like other scientists in X Division, Wen Ho Lee was intensely engrossed in his work and spent most of his time working alone in his office, which was cluttered with the usual assortment of notes, scientific journals and article reprints. Sometimes the code teams got together to talk about problems, but more often than not, the scientists simply met one-on-one with their team leaders.

Outside X Division, Lee led an unremarkable life. He seemed to be an ideal neighbor: quiet, unobtrusive, helpful. He trimmed his trees, cut his grass, kept his hedge clipped and never failed to return tools that he borrowed. The Lees' yard had two apple trees and a cherry tree. "He would often invite us to pick his fruit," says Gordon Spencer, one of his neighbors. "He would say something like, 'Won't you pick our fruit?' or 'Won't you share in our good fortune?'"

He was a devoted father, a soccer dad who ferried his children, a boy and a girl, to games after school and on the weekend. He helped them with their homework, took them to piano lessons and had them take Chinese lessons to make sure they didn't forget their heritage. He loved classical music and fine literature, and often went fishing in the silvery, fast-flowing streams that surround Los Alamos.

Wen Ho Lee was known for his hospitality and his down-to-earth demeanor. When friends dropped by, he plied them with fruit and freshly caught fish and homemade Chinese delicacies occasionally spiced up with New Mexico's famous green or red chiles. One afternoon he brought out a plate of sliced watermelon for some of his children's friends. When one of the youngsters refused to eat the watermelon because of the seeds, he returned to the kitchen, removed the seeds and brought the plate back to the table. The small domestic gesture, imbued with a quiet humility, left a lasting impression upon the youth.

To family members and neighbors, the case against Wen Ho Lee seems like a black comedy, a terrible mistake that has led them to question everything they know about America and its justice system. They can't reconcile the benevolent and caring individual they have known for years with the sinister figure portrayed in government documents and newspaper reports. Jean Marshall, who has lived next door to the Lee family for twenty years and also works at the lab, says Wen Ho Lee never failed to brighten her day with some sort of witticism. "I have loved living next door to Wen Ho," she testified at one of the hearings. "I remember the first time I met Wen Ho. Our houses were just being framed and his fireplace had just gone up, and I remember that he had tacked a picture of his family up on the fireplace. And we went over to meet him, and it was about Christmastime...He introduced himself, he said, 'I'm Wen Ho, like Santa, ho, ho, ho.'"


In December 1982, just a few years after Lee arrived at Los Alamos, the FBI "intercepted" a conversation between him and a scientist at Lawrence Livermore National Laboratory in California who was under investigation for possibly passing classified information to the People's Republic of China. The inquiry was code-named "Tiger Trap." In a closed-door hearing in front of Judge Parker, Robert Messemer, an FBI agent who specializes in counterintelligence investigations, said that Dr. Lee, speaking in Mandarin Chinese, had offered to help the suspect find out who had "squealed" or made "little reports." At the same time that Lee was talking with the Livermore scientist, investigators discovered, he was also calling the Taiwanese embassy in Washington, D.C.

Eleven months later, when the FBI confronted Lee with the information they'd obtained, he denied that he had ever made such a telephone call or had a relationship with the Livermore scientist. "His denials were unequivocal," Messemer related. When the FBI interrogated him again, however, Lee admitted that he had lied and agreed to help the FBI in its investigation.

According to testimony that Attorney General Reno provided to the Senate Judiciary Committee last June, during that second interview, Lee told the FBI that he had been in contact with Taiwanese nuclear researchers since 1977 or 1978. He said he had done consulting work for them and had given them unclassified research papers. "Lee indicated that starting about 1980, he would receive requests for papers and reports from the Taiwanese Embassy, which he would then copy and mail to the embassy," Reno testified. "Lee explained that he contacted the [name deleted] scientist because Lee thought that this other scientist was in trouble for doing the same thing that Lee had been doing for Taiwan, and thus Lee had become concerned."

Reno's testimony, which was released last year after certain information was redacted, highlights one of the still-unexplained aspects of the case: If Wen Ho Lee were purportedly working for another country, was it the People's Republic of China or Taiwan? Relations between the People's Republic and the island province have often been strained, with mainland China insisting upon reunification and many Taiwanese calling for complete independence. Reno alluded to the contradiction in the closed-door Senate hearing, saying that if Lee's contact with the Livermore scientist was being used "to suggest that you are an agent of a foreign power, to wit, the PRC, the immediate question is raised, how are you (a Chinese agent) if you are clearly working with the Taiwanese government on matters that apparently involve non-classified information?"

On January 24, 1984, Lee took a polygraph test, during which he was asked whether he had passed any classified information to a foreign government, as well as about the nature of his contacts with the Livermore scientist. Lee once again explained why he had contacted the scientist and denied passing any classified information to a foreign agent. The polygraph confirmed his truthfulness. On March 12, 1984, the FBI closed its investigation of Lee.

Life returned to normal at X Division. When scientific delegations from China visited the laboratory, Wen Ho Lee's wife, Sylvia, frequently acted as translator. Born in Hunan, China, in 1943, Sylvia had became a naturalized American citizen in 1977. As a secretary and, later, data analyst, she, like her husband, held a Q clearance. Over time, she developed more extensive contacts and closer relationships with the Chinese delegations than almost anyone else in the laboratory. Sometimes the Lees hosted social events for the Chinese visitors at their home. They grew somewhat protective of their foreign guests, and according to a congressional report, Wen Ho Lee "aggressively" injected himself into a gathering on one occasion by insisting upon acting as interpreter for the group.

In 1986 and again in 1988, Wen Ho and Sylvia Lee traveled to Beijing. Both times, Dr. Lee visited the Institute for Applied Physics and Computational Mathematics, where Beijing was developing its own nuclear weapons. The Lees also did some sightseeing, stopping at the Great Wall of China. There was nothing improper about these trips; indeed, Los Alamos was actively encouraging its scientists to exchange unclassified information with their scientific peers in other countries, including the People's Republic of China.

At the same time, counterintelligence officials working at the national laboratories used these excursions to obtain knowledge about weapons development in China and other countries. As Robert Vrooman, a former CIA official and former head of counterintelligence at Los Alamos, explained in a speech last December: "The most difficult thing for an intelligence officer interested in collecting information from scientists is getting continued access. Intelligence officers do not normally mix well in scientific gatherings or social events...Thus intelligence officers have to resort to using friendly scientists to get information for them. This can range from simple interviews after contact with a foreign scientist to elaborate training and preparation."

The U.S. intelligence community knew little about China's nuclear-weapons program until 1979, when a U.S. scientist went to China and found that they were willing to talk about what they were doing. "This visit," Vrooman said, "led to ten years of 'controlled,' let me emphasize the word 'controlled,' contacts between Chinese and U.S. nuclear-weapons specialists. By the early 1990s, the U.S. intelligence community knew the names of the leading Chinese weapons specialists, knew information on the weapons systems and understood Chinese nuclear doctrine."

China had begun working on an atomic bomb in 1953. It exploded its first atomic bomb in 1964 and a hydrogen bomb in 1967. (The United States did not perfect a deliverable hydrogen bomb until 1954, some nine years after the first atomic bomb had been detonated.) According to the Federation of American Scientists, China now has amassed some 2,000 weapons, far fewer than what the U.S. has stockpiled.

Like other Los Alamos scientists traveling abroad, Lee was given a special briefing to alert him to potential risks that he might encounter. When he returned, he filed reports about his visit and was thoroughly debriefed by Los Alamos security officers.

In 1993 and 1994, the laboratory was trying to shrink its workforce, and Lee was notified that he might be one of the people who would lose his job. The "reductions in force," or RIFs, caused great turmoil in Los Alamos: The laboratory was the town's primary employer, and losing your job meant uprooting your family and leaving New Mexico. Lee sent employment inquiries to the National University of Singapore; Nanyang University, also in Singapore; the Swiss Defense Technology Procurement Agency in Switzerland; Messerschmitt Bolkow-Blohm in Germany; Chung Chang Institute in Taiwan; Cheng Kung University, also in Taiwan; and the Hong Kong Institute of Science and Technology.

When Lee survived the cutbacks, he didn't pursue these opportunities. But Sylvia was not so lucky: She was involuntarily terminated in 1995 during another workforce reduction. According to an August 1999 joint statement by the Senate Governmental Affairs Committee, Sylvia Lee's personnel file contained incidents of alleged security violations and threats she had made against co-workers, but no details were provided on the nature of those violations or threats. (A civil lawsuit subsequently filed by the Lees against several federal agencies states that Sylvia had actually been recruited by the FBI to help monitor Chinese scientists. "Sylvia Lee never requested any payment from the FBI when she put herself and her husband at risk to help protect America's national security," the suit notes.)

In 1995, the year that Sylvia lost her job, the CIA received a classified Chinese report containing information about several U.S. thermonuclear weapons, including the W-88, a cone-shaped thermonuclear warhead launched from missiles carried aboard the Trident submarine. Some 4,000 to 5,000 of the W-88 warheads were to be manufactured at the Rocky Flats Nuclear Weapons Plant outside Denver, but production had been halted in 1989 after the FBI raided Rocky Flats. Although the CIA concluded that the person who'd leaked them the document was actually a Chinese agent, it nevertheless pulled together a group of experts from the Department of Energy and the weapons labs to analyze the data.

The DOE, which operates the nation's three nuclear-weapons labs, focused only on the W-88 warhead. Investigators concluded that information about the warhead had been passed to China sometime between 1984 and 1988 and that the person who provided the information probably worked at Los Alamos, where the weapon had been designed. Government officials then performed what's called a "matrix analysis." Three lists of people were compiled: scientists from Los Alamos who had access to the design information; scientists who had traveled to China between 1984 and 1988; and those who had contact with visiting Chinese delegations during that period. One major suspect popped up: Wen Ho Lee.

But that analysis was "seriously flawed," according to Vrooman, the former Los Alamos counterintelligence head, with not one shred of evidence linking Dr. Lee to the theft of the W-88. "The DOE investigators developed a long list of [Los Alamos] travelers, seventy names, which still turned out to be woefully incomplete," he said in another speech. "They reduced this to twelve suspects, with Lee as the only real candidate. I did not question why Lee was on this list, as he met the criteria, but I did question why several others were on the list. Three had no access, and one did not even have a clearance. The lead investigator told me that he was sure that Lee was the one, and only needed other names to fill up the list."

Vrooman, who, along with two others, was subsequently criticized by the DOE for failing to follow through on certain actions with regard to Lee, said the information obtained by the Chinese was also available on many classified documents distributed to hundreds of locations throughout the government and its complex of contractors. For example, one document containing a rather detailed description of the W-88 had 548 addresses on its distribution list.

Nonetheless, the DOE forwarded the results of the inquiry, dubbed "Kindred Spirit," to the FBI. The bureau opened its investigation in May 1996; after reviewing all of the material, the FBI concluded that it was indeed possible that Lee had passed information about the W-88 to China. But the supporting documentation, as Vrooman -- and later even Reno -- would note, was scanty: The evidence included Lee's involvement with the Livermore scientist in the early '80s, some software and calculations related to hydrodynamics that he'd purportedly supplied to the Chinese, and his work on nuclear-weapons source codes, which were of increasing interest to China since it had stopped actual testing. In addition, the Lees apparently had been treated well during their visits to China, and the FBI saw this as "standard PRC intelligence tradecraft" to encourage Chinese living abroad to visit ancestral villages and family members as a way of "trying to dilute loyalty and encouraging solidarity with the authorities in Beijing."

But the investigation into Wen Ho Lee soon got bogged down in a series of miscommunications and missteps involving Los Alamos, the DOE, the Department of Justice and the FBI. The bureaucratic bungling, as well as China's alleged espionage, would eventually become the subject of numerous congressional hearings. Even former Denver mayor Federico Peña would be dragged into the furor.

Peña, who had served as Secretary of the Department of Transportation during Bill Clinton's first term, was named Secretary of the Department of Energy at the start of Clinton's second term. He says he was flabbergasted when, in 1997, he heard allegations of espionage within the DOE. "The notion that espionage was occurring in our nuclear laboratories was shocking and disturbing," he recalls.

Upon learning of the allegations, Peña says he alerted key officials within the White House, the Department of Defense, the Central Intelligence Agency and the Office of the Attorney General. He also reorganized the intelligence-gathering functions within the Department of Energy, creating, in effect, a new office of intelligence and a new office of counterintelligence that reported directly to him. In addition, Peña says, he recruited Ed Curran, formerly with the FBI, to head up counterintelligence operations and doubled that budget.

"This was a major change within the Department of Energy," Peña recalls. He summoned the directors of the national laboratories to Washington, where they were briefed on the espionage allegations not only by him, but also by FBI director Louis Freeh and CIA director George Tenet. "We wanted to make sure the message was delivered very clearly," Peña says.

The DOE also provided assistance in the espionage investigation of Peter Lee and implemented numerous other changes. "We did these things in a quiet fashion," Peña adds. "We did not want to alert any suspects."

Peña resigned the DOE post and returned to Denver in mid-1998.

In the spring of 1998, Dr. Lee spent six weeks teaching and consulting at the Chung Shan Institute of Taiwan, a government-owned organization that specializes in national defense technologies and information. He returned to Taiwan again in December 1998 to deliver a speech at the institute and do some more consulting. During one of these trips, he accessed the Los Alamos computer from a remote terminal called "Seagull," removed two unclassified files from one of his classified collections of files, and had the two documents electronically transferred back to Taiwan.

On December 23, 1998, Lee was administered another polygraph examination, officially known as a Psychophysiological Detection of Deception Examination, by the Wackenhut Corporation, a DOE contractor. According to a copy of the examination in the appeals-court files, the test had been requested by Edward J. Curran, director of the DOE's Office of Counterintelligence, in order to "resolve a security concern." The almost-six-hour examination was given in a large conference room at Los Alamos; voices and other workaday sounds could be heard, but they didn't seem to distract Lee.

During the exam, Lee talked about the lie detector test he had taken in the early '80s, relating basically the same story that agent Messemer had told Judge Parker during the closed-door hearing. Lee also told the polygrapher that at about five o'clock one evening in August 1998, while working at his office, he received a strange call from a man he had never met before. The caller said he was from China and was staying in a Santa Fe hotel. "Does the Peter Lee case result in any consequences to the Chinese at the laboratory?" the caller asked.

Taiwanese-born Peter Lee is another scientist who'd worked at Los Alamos and for a contractor to Lawrence Livermore labs. He is not related to Wen Ho Lee, nor is he the Livermore scientist whose phone was tapped in the early '80s. According to a report issued by a select committee chaired by California Republican Christopher Cox, during a 1985 trip to China Peter Lee provided the People's Republic with classified information on how lasers are used to create miniature nuclear fusion explosion; in 1997, he is alleged to have provided them with information about submarine detection research. Peter Lee pleaded guilty in 1997 to wilfully passing classified U.S. defense information to the People's Republic during his 1985 visit and to falsifying reports of contact with PRC nationals in 1997. He was sentenced to twelve months in a halfway house, a $20,000 fine, and 3,000 hours of community service.

Dr. Lee found it strange that the caller was asking him a question about Peter Lee. "Nothing happened," he responded. Then the caller asked Lee to meet him at his hotel; Lee said he would have to obtain approval from the lab first. "That's fine, get your approval," the caller instructed. But Lee thought about it, told the man he was not interested and hung up. The next morning, he said, he told the appropriate lab officials about the conversation.

(The phone call turned out to be a "false flag operation" -- with an intelligence agent pretending to be from another country -- designed by the FBI to get the Wen Ho Lee case off dead center, according to a person familiar with the investigation. But Dr. Lee did not take the bait.)

As the polygraph continued, Wen Ho Lee apparently disclosed for the first time that during one of his trips to China in the late '80s, a "Mr. Chin" had asked him a question that he knew pertained to classified information. A "Mr. Hu" was also present for the interchange but didn't say anything. "Mr. Lee stated that when Mr. Chin asked this question, he responded that he did not know and that the question did not interest him," the examiner noted.

Lee's failure to mention this contact earlier seems like a small detail, but security regulations require Los Alamos scientists to inform their superiors whenever a foreign scientist tries to elicit classified information from them. Dr. Lee initially "inferred" that he had reported the discussion with Mr. Chin on his trip report, the polygraph states, but subsequently admitted that he may not have specifically mentioned it. He also told the examiner that for several years after the conference, he had received requests from "various professionals" requesting information that was previously published or in the public domain. "He said he honored such requests but specifically identified public domain information," the examiner stated. "He never provided any other information, and absolutely no information of a sensitive or classified nature." The examiner then asked Lee four specific questions:

"Have you ever committed espionage against the United States?"

"No," responded Lee.

"Have you ever provided any classified-weapons data to any unauthorized person?"

"No."

"Have you had any contact with anyone to commit espionage against the United States?"

"No."

And finally, the interviewer asked, "Have you ever had personal contact with anyone you know who has committed espionage against the United States?"

"No," Lee replied.

The examiner concluded that there was "sufficient physiological criteria to opine that Mr. Lee was not deceptive when answering the questions." In other words, Lee was telling the truth. But because he did not fully disclose his foreign contacts, DOE headquarters in Washington nevertheless advised Los Alamos to transfer Lee from X Division to T Division, where theoretical studies were done.

The FBI's investigation of Lee intensified in early 1999. The FBI interviewed him on January 17 and again on February 8 and 9. On February 10 he took two polygraph examinations. This time an FBI polygrapher from Washington, D.C., was flown in. The tests were conducted in an Albuquerque hotel room. It was hot in the room, above 72 degrees. The FBI examiner stood behind Lee, operating the machine. "On the first set of examination questions, he indicated inconclusive responses. On the second polygraph, he indicated deception," FBI agent Messemer testified before Judge Parker. The deception, he added, occurred when Lee was asked whether he had gathered information related to the W-88 and whether he had unlawfully transmitted any classified information to a third party. Messemer later testified that during the FBI polygraph, Lee revealed "yet another instance where he had provided assistance to another PRC scientist who he knew to be involved in PRC weapons development."

A number of factors could have affected the outcome of these polygraph tests. The FBI apparently had told Lee they wanted to test him in order to assist the bureau in solving a "puzzle related to the W-88." But when he sat down for the tests, the polygrapher informed him that the true purpose was to determine whether Lee should be criminally prosecuted.

Lee reportedly became extremely upset. The emotional agitation, Messemer conceded under cross-examination, could have led to unreliable results. The data also could have been skewed by the fact that a person whom Lee didn't know was asking about highly classified information in a hotel room that was not safe from eavesdroppers, Messemer admitted.

"Do you know that the polygrapher put wires around Dr. Lee's thumb and arm in such a way that he actually was in physical pain and his thumb went numb during the polygraph?" Mark Holscher, Lee's defense attorney asked. "I wasn't aware of that," Messemer responded.

The FBI again interviewed Lee on March 5. That same day, Lee's offices in X Division and T Division were searched, and authorities discovered he had made some alterations on three classified documents. Using his computer, Lee had deleted the classification marks on a chapter of a reference manual to make it appear unclassified. He had covered up the classification marks on another document and then Xeroxed it so that it, too, appeared unclassified. And on a third, he had used scissors to physically remove the classification marks at the top and bottom of the page.

Before Judge Parker, Messemer testified that the removal of classification markings was suspicious because it "facilitates" the movement of classified information without detection. But Holscher pointed out that Lee apparently used the three documents on a daily basis. Numerous scientists at Los Alamos found the security precautions a hassle. Wasn't it possible, he asked Messemer, that Lee changed the classification marks in order to avoid having to lock the documents in a safe each night? "I suppose that inference could be drawn," the agent responded.

The day after Lee's office was searched, the New York Times published a front-page story detailing how China purportedly stole the W-88. The article did not identify Lee by name, saying only that a Los Alamos computer scientist of Chinese descent had been identified as a suspect. But in a small town like Los Alamos, it was not hard to figure out who that suspect was.

The following day, a Sunday, FBI special agents Carol Covert and John Hudenko questioned Lee again. This time the interrogation got ugly; the two agents appeared to be angling for a confession. They urged Lee to come clean about his contacts with the Chinese nuclear-weapons scientists. If he didn't, they warned, his life would be ruined. His children's lives would be ruined. He could even wind up in the electric chair like those traitors Julius and Ethel Rosenberg.

Although Lee had passed the DOE-administered polygraph, the two FBI agents told him that he had failed. "You failed, Wen Ho!" one shouted. "You failed everything!" The interview went on and on, but Lee stood his ground.

Agent: "Look at it from our standpoint, Wen Ho. Look at it from Washington's standpoint... you have an individual that's involved in the Chinese nuclear weapons program. And they come to your hotel room, and they feel free and comfortable enough to ask you a major decision about [deleted]."

Lee: "Uh, mmm."

Agent: "And then in 1994, they come to the laboratory and they embrace you like an old friend. And people witness that, and things are, are observed, and you're telling us that you didn't say anything, you didn't talk to them, and everything points to different than that."

Lee: "Well..." (sighs).

Agent: "So, you know, I mean, it's, it's, it's, it's an awkward situation that I, I can understand, you know, where, where these things could happen. I mean, you were treated very nicely in 1986 when you went to China."

Lee: "Uh, hum."

Agent: "I mean they were good to you. They took care of your family. They took you to the Great Wall. They had dinners for you. Then in 1988 you go back and they do the same thing and, you know, you feel some sort of obligation to people, to talk to them and answer their questions...You gotta understand this is the way it is ...You're being looked at as a spy!"

Lee: "Yes, I know, I know what you think, but all I'm saying is, uh, I have never say anything classified. I have never say anything."

Agent: "It might not be that, Wen Ho. It might not be even a classified issue. It might just be something that was said, but Washington is under the impression that you're a spy. And this newspaper article is doing everything but coming out with your name."

Lee: "Let me ask you this. OK? If you want me to swear with the God or whatever, OK? I can swear if that's what you believe. I never tell them anything classified. I never told them anything about nuclear weapons..."

Agent: "What happened, Wen Ho, something else had to have happened in that motel room. Something had to have happened when they came to your room. Because it's, it's just logical...We know how the Chinese operate...we know..."

Lee: "What do you mean, what do you mean?"

Agent: "Something happened in that room that you're not telling us?"

Lee: "This is what I'm saying, OK? You know, we may chat something social, OK? I don't remember what we have said in that room in the hotel, OK?...All I can remember is when they asked me this question [material deleted]. I told them I don't know and I, I am not interested to discuss. And then we switched to different conversation. I don't even remember what we said before or what we said after. I mean it's such a long time, but I know it's nothing to do with the technical. OK?"

Agent: "You are a scientist, a nuclear scientist. You are going to be an unemployed nuclear scientist. You are going to be a nuclear scientist without a clearance. Where is a nuclear scientist without a clearance going to get a job?"

Lee: "I cannot get any job."

Agent: "You can't! Wen Ho, you gotta tell us what went on in that room. You got to tell us why you're failing these polygraphs! Washington is not going to let you work in a laboratory or have a clearance!"

Lee: "I can retire...I'm 59 and something..."

Agent: "Do you really think you're going to be able to collect anything?"

Lee: "No, no, but look, look, look..."

Agent: "They're going to garnish your wages...They're not going to give you anything other than your advice of rights and a pair of handcuffs!"

Lee: "But, but..."

Agent: "And now, what are you going to tell your friends? What are you going to tell your family? What are you going to tell your wife and son? What's going to happen to your son in college?"

Lee: "I never give any classified information to Chinese people. I never tell them anything relating to nuclear weapons, uh, data or design or whatever, I have never done anything like that."

Agent: "Pretty soon you're going to have reporters knocking on your door. They're going to be knocking on the door of your friends. They're going to find your son and they are going to say, you know, your father is a spy?"

Lee: "But I, I'm not a spy."

Agent: "But Wen Ho, something else must have happened for you not to be able to pass these polygraphs."

Lee: "I don't know, I don't know what to explain. I did not tell them anything about [deleted]. I told them, I say, I...let's see. I don't know and I'm not interested to discuss this question. That's exactly what I told them."

Agent: "You know what I believe? I believe that you're not telling me the truth. I believe something else happened in that room and that's why you're failing the polygraph. And unless you can come up with what happened in that room, part of a conversation that's causing you problems, you're never going to pass a polygraph. And you're never going to have a clearance. And you're not going to have a job. And if you get arrested, you're not going to have a retirement."

Lee: "Well, OK, let's, let's stop here cause I'm very tired, OK, I'm, I'm..."

Agent: "Do you know how many people have been arrested for espionage in the United States?"

Lee: "I don't know. I don't pay much attention to that."

Agent: "Do you know who the Rosenbergs are?"

Lee: "I heard them, yeah, I heard them mention."

Agent: "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: "Yeah, I heard."

Agent: "They didn't care whether they professed their innocence all day long. They electrocuted them. OK. Aldrich Ames. You know Aldrich Ames? He's going to rot in jail."

Lee: "OK, I told you before. I don't belong to any religion. I don't go to church. Well, I mean once in a while, but I don't believe in God, OK. However, I think there must be a something like a God, OK. Not may not be a Christian God, but something like that, you know, super power, super creature...round the universe, and I believe he will make the final judgment for my case. And I depend on him. I don't depend on you or depend on [name deleted] or depend on Washington people. I don't depend on this, I depend on this God. I think he will make a final judgment."

Agent: "You know what, the Rosenbergs said that, too."

Lee: "I don't..."

Agent: "The Rosenbergs professed their innocence. The Rosenbergs weren't concerned either."

Lee: "Yeah."

Agent: "The Rosenbergs are dead."

Lee: "I'm just telling you. I believe truth and I believe honest, and I know, I know myself, I did not tell anything...I believe this super creature will make a judgment on this whole situation and eventually something will be clear-cut, OK?"

Agent: "You know, Wen Ho. This super creature up here? He can make whatever decisions he wants to make, OK?"

Eventually, Lee summoned up his courage and told the agents he was going to walk out of the interview. But before he did, he told a long, rambling story that he hoped would explain why he'd forgotten certain details about his two visits to China. When he was sixteen, he began, he had his appendix removed. Although he had always had a wonderful memory, he couldn't memorize or retain a thing for the year following the operation. Then in 1987, he underwent a second surgery, for cancer of the colon. He suffered the same inexplicable memory loss again, only this time it was much more severe because he was older.

That's why he probably did not recall everything about his meetings with the Chinese weapons scientists until ten years later when he underwent the polygraph, he told the agents. "When human being is forced to do some more concentration, like when people do polygraph on you, you will concentrate, concentrate," Lee said. "And you can think about something, which in the ordinary time you don't remember. But for that particular moment, you may remember something. Just pop up. And that's what happen to me, OK? You won't take it? It's up to you. I have no other choice, I just have to trust this superman on the universe..."

But Lee's superman did not come through for him. On March 8, the day after the grueling FBI interview, his security clearance was terminated and he was fired from his job. Energy Secretary Bill Richardson, who'd replaced Peña, said the firing had nothing to do with the fact that the story on Chinese espionage had appeared two days earlier in the Times.

At this point, the case against Lee still looked shaky: a few security infractions, an understandable memory lapse, some tantalizing coincidences. Several FBI agents considered the case so flawed that they'd written memos to their superiors outlining their concerns.

But suddenly, the investigation veered into fertile new territory. While reviewing the contents of Lee's office, Los Alamos physicist John Romero happened to spot a directory printout on his desk. The directory contained the names of virtually all of the laboratory's nuclear-weapons source codes and related files. At first Romero thought the document had been printed off of the Los Alamos secure network, which would not have been unusual. Then he realized the document had been printed from a directory sitting on the lab's unclassified network -- a system that was accessible from the Internet and vulnerable to hackers. Romero did a double take. "I couldn't believe it. I just couldn't believe it," he would later testify.

The espionage investigation suddenly morphed into a related inquiry into Lee's mishandling of vast amounts of classified data. This new inquiry would turn out to be the largest forensic investigation in the FBI's history. All through the spring, summer and fall of 1999, agents sifted though millions of bytes of data stored on the logs, disks, tapes and hard drives of Los Alamos's vast computing system. By the time it was over, they had conducted 1,000 interviews and studied four terabytes of information. (Printed out and stacked, four terabytes of information would be equal to 122 Washington monuments, or roughly half of the information contained in the Library of Congress.) In the end, it was discovered that the genteel, soft-spoken Dr. Lee had downloaded "all the codes, all the data, all the input files, all the libraries, the whole thing is there, the whole ball of wax, everything," Romero said.


In the early '90s, Los Alamos National Laboratory's computing system was in a state of transition. As public access to the Internet expanded, the weapons lab, which has some of the largest and fastest computers in the world, began putting up firewalls to protect its vast treasure trove of classified data. At one point all of the lab's information, classified and unclassified alike, was stored on a single network, with a system of software and hardware separating the secret data. By 1993 and 1994, the period in which Lee did most of his downloading, the lab's one network had already been broken into two pieces: a red partition, reserved for secret, restricted data, and a green partition, which contained open and unclassified information. A vast archival data-storage system, known as the Common File System, was accessible from both networks. Q-cleared scientists working in the red partition could go through a bank of switches to the green network and then connect with the world beyond. But for security reasons, it was not possible to go from the Internet to the green network and back up into the red partition.

Using logs maintained by Los Alamos's various computers, FBI experts were able to reconstruct in great detail how Wen Ho Lee had used the laboratory's interlocking computer system to move data around. He would first log on to the classified network, then issue a "TAR" command to the computer. This command, which acts like a bucket, would instruct the computer to scoop up dozens of files, subfiles and directories on a certain topic and group them together as one file. After saving the TAR file back to his directory on the secure network, Lee would then call up the file again, type in "CL=U," and resave the file. Now the file was marked as an unclassified file, but it was still a red-partition file and located in the red-partition area.

Next, Lee would log on to "Machine C," and down-partition the TAR files he had collected from the red to the green network. Machine C, which eventually was removed from Los Alamos, was dedicated almost solely to down-partitioning files from the red to the green network. Q-cleared scientists who accessed this computer were basically on the honor system; simply by logging in and using the machine, they were certifying that the information they were downloading was unclassified.

After down-partitioning the files to the green network, Lee would then would log on to "Machine Rho," a Cray supercomputer in the unclassified area, bring down the file he had just converted, and save it back into his green directory. He then would go back and delete the interim versions marked as unclassified that he had saved on his red directory.

But the process was not yet complete. Lee still had the portable tapes to make. Smaller and thinner than a videotape, the tapes held 115 megabytes of information and could easily be carried out of X Division -- past the guards and through the security gates -- in a scientist's suitcoat. Lee's machine didn't have a tape drive connected to it, however, so he went to an employee who worked in a trailer outside the secure area and asked if he could use his machine to download his resumé. The employee readily agreed, booting up his computer to show Lee how the machine worked and even going so far as to write down his login and password. According to testimony, Lee then returned to the trailer on multiple occasions, mostly during lunch hour or at times that he knew the employee would be away, to make the tapes. The trailer was sometimes left open 24 hours a day, and the computer, which was dubbed "ctrssl," was vulnerable to the most unsophisticated of hackers.

By the time he was through, Lee had assembled some nineteen TAR files containing millions of bytes of data. Seventeen of the TAR files were downloaded to nine portable tapes. A tenth portable tape was created in 1997, from information downloaded directly from the secure network.

Cheryl Wampler, a computer specialist at Los Alamos, said it probably took Lee some forty hours over seventy days to transfer the nineteen classified files he is accused of mishandling. "This required considerable effort," she testified. FBI agent Messemer also testified that Lee had gone to considerable effort to make sure that the material he was downloading would fit exactly onto the tapes. "It didn't appear to us as investigators that he was simply sending everything...He took very good care to find which files he specifically wanted to assemble into the TAR files."

Dr. Lee's private collection comprised a veritable library of the most up-to-date thermonuclear weapons ever designed by Los Alamos. There was no other library in the world like it, save those at the Los Alamos and Lawrence Livermore laboratories. Physicist Richard Krajcik said he was deeply shaken when he learned what had been transferred: "When I first realized what was downloaded by Dr. Lee, I realized that I was looking at a chilling collection of codes and files. Chilling in the sense that it contained the codes important to doing design or design assessment, files important to determine geometries, important successfully tested nuclear weapons...It contained devices across a range of weapons, from weapons that were relatively easy to manufacture, let's say, to weapons that were very sophisticated and would be very difficult to manufacture...It was all there."

Wen Ho Lee downloaded in their entirety the primary and secondary codes that were used on a daily basis to monitor and access the reliability of America's nuclear stockpile. Specifically, he downloaded "Code A," an alias for a secondary code that is some 223,000 lines in length. Furthermore, according to testimony, he allegedly downloaded both versions of the code, one that could be run on a Cray supercomputer and one that could be run on a more portable Sun computer or even a Hewlett-Packard. He also took the data tables needed to run Code A in two different computer formats. Code A, testified physicist Stephen Younger, was the lab's "key design tool."

Lee also downloaded "Code B," a modern primary code that was also used on a daily basis. Code B and its related databases, Younger testified, "represent a complete nuclear-weapons design capability, everything you would need to install that capability in another location, everything."

He also took Codes D, G, H, K and I, as well as the related data tables and the so-called input decks, or blueprints, for numerous types of weapon designs, ranging from the most rudimentary to the most sophisticated design in the arsenal. Said Krajcik, "It wouldn't be so much that you wouldn't expect a code physicist to have some of these input decks. What I found surprising was that he had a whole collection of important input decks, decks of devices that had been successfully tested."

The Los Alamos physicists testified that there was no legitimate reason for one scientist to have amassed all of the codes, since they generally worked on only one small piece at a time. There was also no need for scientists to make backups, because numerous protective measures had been built into Los Alamos's computing system so there was zero chance that the information could be lost.

All of the Q-cleared scientists, including Lee, were well-versed in the rules of security. Many had been in the program long enough to have witnessed actual detonations at the Nevada Test Site or at the Pacific Proving Ground, and they understood how necessary it was to protect the information. Nobody in the history of Los Alamos had ever moved such a vast amount of data to an unclassified environment, Krajcik testified. "People who work on these codes work in a classified environment for a specific reason, and that is that they are dealing with extremely sensitive materials."

As the computer investigation proceeded, the FBI also discovered that Lee had begun deleting the classified files he'd collected just as the authorities were closing in. In all, 360 files were deleted, including the nineteen TAR files. The deletions occurred on January 20, February 10, February 11, February 12 and February 17. One of the largest deletions was made only two hours after Lee had been notified that he failed the FBI polygraph.

Investigators also discovered that during this period, Lee had reconfigured several of the tapes that he had made to remove the classified material. According to Messemer, Lee lied to another employee in order to get access to a machine with a tape drive, telling the employee he needed to upload the information on the tape "into the unclassified system in order to run some calculations," the agent testified. "Moreover, [Lee] said that he would make a copy of these calculations available to the T-3 user of this computer, ostensibly to allay any concerns he might have that Dr. Lee was using it improperly."

With the massive deletions, Wen Ho Lee almost succeeded in obliterating his tracks forever. Reconstructing the files was a veritable "needle-in-a-haystack operation," Messemer said. "We came very, very close, within literally days, of having lost that material."

"Permanently?" asked Robert Gorence, the lead prosecutor.

"Permanently," Messemer responded.

"I don't want to put words in your mouth, but if they had been permanently deleted and written over on the central file system, would that deletion by Dr. Lee have kept that forever from this investigation?"

"Yes, it would have," responded Messemer. "It would have been irretrievable from our current capability."

One of the items that helped investigators reconstruct the files was a notebook found in Lee's house during an April 10, 1999, search. In the notebook, written in Chinese and English, they found a description of the tapes he had made, the amount of data stored on them, his passwords and a step-by-step set of instructions on how to make the actual tapes. The FBI also found three letters in Lee's garage from Li Deyuan, a senior nuclear-weapons scientist at China's Institute of Applied Physics and Computational Mathematics, and Zheng Shaotang, another senior official from the institute. The letters specifically asked Lee to send unclassified Los Alamos codes to them or to another institute member who was studying at Princeton University. Although at the time the DOE was actively encouraging its scientists to share these unclassified codes in order to create a spirit of cooperation, the letters bolstered the FBI's belief that Lee was engaged in suspicious activities.

The computer forensics investigation also revealed one more thing: There had been some sixty to seventy incidents in which someone sitting at a computer at the University of California at Los Angeles had used Dr. Lee's login and password. Many of these logins occurred at nearly the same time that Lee was downloading and transferring data.

According to Lee's defense attorneys, he had given his login and password to his two children, who were using them to log on to the Internet. While their activities may have been innocent, it made the data sitting on Los Alamos's open network more vulnerable to hackers. Scott Larson, an FBI agent who supervises the bureau's "Infrastructure Protection and Computer Intrusion Squad," testified that hackers gravitate to university computers because scientists who are teaching classes often use these machines to connect with their employers. "It's part of the methodology," he said. "If I want to attack a particular Air Force base or lab, I'm going to first hack into a university close by, where people are taking classes and quite often log in back and forth from the university account to their military account or lab account."

Lee's login and password had also traveled across the open Internet when he was in Taiwan and had the two unclassified files sent back to him. Larson said he had "a suspicion" that Lee's login and password had been captured. "Whether it's been used or not, I don't know," he testified. "And the methodology would be to use an account that has root access, grab the files and then delete any sort of track."

According to government witnesses, one of Lee's passwords was "W. H. Lee," which FBI agents said provided no extra protection whatsoever. "The use of his name as a password was functionally as if he never used a password because it would be so easy to guess by an outsider or unauthorized person to gain access to those secret, restricted data files," Messemer testified.

What would all of this information mean in the hands of another country? Physicist Stephen Younger testified that it would mean different things to different nations. If a country that had not yet developed a workable atomic bomb obtained the tapes, it could develop a credible weapon in a short period of time without having to do any actual testing. Countries that were a little further along could greatly advance their nuclear-weapons capability. And those countries with a fully developed weapons program could use the data to pinpoint "vulnerabilities in the American arsenal, which would help them to defeat our weapons through antiballistic missile systems or other means," he said.

Paul Robinson, the hawkish director of Sandia National Laboratories and advisor to the commander in chief of STRATCOM, concurred with Younger's assessment, testifying that the loss of the tapes was one of the most serious breaches of national security that he had ever seen. "These tapes could truly change the world's strategic balance. The previous worst case I am aware of classified information being stolen also happened at Los Alamos, [with] Klaus Fuchs taking a design that if detonated, could demonstrably kill 100,000 people in a city. These would allow the design of weapons that would kill several million people if a single weapon were detonated in a city. In that sense, it raises the level of danger and concern."

If the government does not ascertain who might have seen the actual data, Robinson testified, U.S. military planners will have a much harder time trying to assess threats. Hinting at how the government might attempt at trial to show Lee intended to harm the U.S., prosecutor Robert Gorence then asked, "Is a mere uncertainty of a risk of harm an injury to the United States?"

"I believe the United States is already harmed," Robinson replied.

"Would you contemplate the United States government spending -- and I don't want to mischaracterize it, but enormous amounts of money in response to what Dr. Lee did?"

"The United States would do everything in its power to preserve freedom. I am not sure at this point exactly what the next step is that we would take. This is a grave undercut to our strategic posture."


The missing tapes were a catch-22 for Lee's defense team. After losing his security clearance, Lee had certified on a boilerplate Security Termination Statement that "in accordance with DOE security regulations, I have destroyed or transferred to persons designated by the DOE all classified documents and material for which I was charged or which I had in my possession." Investigators found this statement inadequate, and demanded specific details on how Lee had destroyed the tapes. But any additional information Lee provided would have incriminated him on the very charges for which he was to be eventually indicted.

Government prosecutors had no evidence that the tapes had been passed to a third party. But the massive computer forensics investigation also had not revealed any evidence regarding the whereabouts or purported destruction of the missing tapes.

And during the bail hearings, neither side offered a motive for why Lee had made the tapes in the first place. Lee himself was rather vague when asked this question during a 60 Minutes interview that aired on August 1, 1999: "The reason I download the computer code from classified machine to -- into unclassified machine is part of my job, to protect my code, to protect my file. I do that routinely. I had never give those, you know, information to any unauthorized person."

During the two bail hearings, Lee's attorneys continued to suggest that the scientist could have downloaded the data in order to protect his work from a computer crash. They also pointed out that most of the downloading occurred in 1993 and 1994, when Lee had been told his job might be eliminated, intimating that perhaps Lee was going to use the tapes in connection with his job search. (The tenth tape, however, was made in 1997.)

Other parts of the case didn't add up, either, the defense team argued. The TAR files had sat on Los Alamos's open network for five or six years, and if Lee had truly been up to something nefarious, why didn't he delete the files, or at the very least, change the names so that nobody would discover what was in them? After all, it was no secret among the Los Alamos scientists that supervisors used computer logs and various electronic monitoring systems to pick up unusual behavior. In fact, one such system, the Network Anomaly Detection and Intrusion Reporting system, or NADIR, had flagged Lee's activity, but the Los Alamos employee who reviewed the report attributed the file movement to the changing computing environment.

The defense team also raised the possibility that Lee began deleting the classified files because without his clearance, he was no longer authorized to have them in his possession. Lee had even contacted the Los Alamos computing center for help with the deletions, which was hardly in keeping with the clandestine behavior of an espionage suspect.

But Richard Krajcik thought Lee was being rather clever when he moved the files from the red partition to the green partition. As Lee transferred the files, he put a password on them, which meant that only the administrator of the unclassified partition would have had access to them. And that person, Krajcik explained, would not have understood the significance of the names even if he or she had seen them. Likewise, the computing people to whom Wen Ho Lee turned for help when he was deleting files also would not have understood what the names meant, Krajcik said.


Once the FBI learned the magnitude of what was on the tapes, Lee was put under around-the-clock surveillance. Since initially their primary concern was recovering the tapes, Messemer said, authorities chose not to swoop down and arrest the scientist. "There was very great debate about this particular topic," he testified. "It was determined that national security interests outweighed the successful criminal prosecution of this matter insofar as it was determined that we needed to get these tapes, get them back to the proper authorities."

The agents parked outside Lee's modest home for months, monitoring his every move and keeping track of all of his visitors. Lee went about his business, enduring the intrusion as best he could. "He told me it was sometimes hard to sleep with them right outside the door, but he came, I think, to take it in stride as graciously as I can imagine any person doing," remembers neighbor Jean Marshall. When Lee left on a fishing trip, four or five cars tailed him. "Finally, into the summer, he was telling me stories like how much the young people that were trailing him enjoyed when he went fishing because they could finally get out of those hot cars they had been sitting in for hours and sit on the bank, and they enjoyed visiting with each other. He said, 'You know, it's good for me to take them fishing.'"

The media also camped out in front of Lee's home, hoping to photograph the alleged spy. For the neighbors, it was hard to figure out who they loathed more: the FBI or the reporters. FBI agents revved their engines at night during their shift changes and shined their lights into bedroom windows, Gordon Spencer recalls. The reporters, on the other hand, blocked driveways and created "sanitation nuisances."

After months of uncertainty and numerous media stories intimating that the espionage investigation had fallen apart, on December 10 a federal grand jury returned a 59-count indictment against Wen Ho Lee, charging him with violations of the Atomic Energy Act and the Espionage Act. The indictment claimed that Lee "acted with the intent to injure the United States and with the intent to secure an advantage to a foreign nation." With cameras rolling and the neighbors looking on in disgust, the diminutive scientist was led from his home in handcuffs and booked into the Santa Fe jail.

During one of the bail hearings, agent Messemer said that Lee had become an even greater threat to the United States after his arrest because he might be motivated to give the tapes to an enemy out of revenge. In addition, there was no way to make sure that he didn't communicate the whereabouts of the tapes to a third party. "We would have to have literally a team of Chinese-speaking agents and translators working around the clock," he said.

Even with intensive monitoring, Messemer said, the FBI couldn't prevent Lee from communicating the whereabouts of the tapes. "In counterintelligence investigations," he explained, "we often find instances of what we call paroles -- that is, a statement that is made by one party to another to establish the bona fides of the third party. And essentially it could be something like, 'How is the weather today?'...It could be as simple as, 'Say Uncle Wen says hello,' that is the message that is given to the right party who understands now they are to do something with those tapes...Even the most simple innocuous messages, even messages of appearing to be nothing but goodwill and gestures of goodwill have to be taken with a grain of salt, if you will, and have to be examined and reevaluated to see whether or not there is something that is insidious."

But Holscher said Messemer's statements were absurd. "This scenario that is being strung here of spies and the inference that Dr. Lee will commit a death-penalty offense while under the most heightened security ever in the United States is just a ludicrous premise," the defense attorney argued.

Judge Parker was confronted with a difficult choice. Lee was a responsible husband and father who had no criminal record, and ordinarily, he would have been released on bail. But this was no ordinary case. The judge had listened to days of apocalyptic testimony about the enormous threat that Lee posed to the entire nation. Sandia's Paul Robinson had likened the choice to a "you-bet-your-country" decision. Directing his comments to the bench, Robinson had warned, "I would take, if it were in my power, every action I could take to make sure this information that has been taken out of its protection is placed back into protection and is not divulged to anyone else. I would be willing to take whatever actions I could to make sure that it does not get transferred to another nation or power."

In the end, Parker ruled that Lee should remain incarcerated: "The government has shown by clear and convincing evidence that there is no combination of conditions of release that would reasonably assure the safety of any other person and the community or the nation."


While Wen Ho Lee has been locked away in jail, support for him has grown steadily. Many Asian-Americans feel that he has been unjustly targeted and that his incarceration is unduly harsh. There have been marches and speeches and a Web site established in his name. Energy Secretary Richardson, who gave the order to fire Lee, has vehemently denied that race had anything to do with the charges, and he recently ordered the entire weapons complex to "stand down" for an afternoon to listen to lectures about race issues.

Only days after the indictment was handed down, Lee fired the first volley of what could become protracted civil litigation. Brian Sun, a Los Angeles attorney, filed a complaint in the District of Columbia against the Justice Department, the FBI and the DOE, claiming that the agencies violated the Privacy Act by "willfully and intentionally" leaking private information about Wen Ho and Sylvia Lee to the media. Dr. Lee, the petition continued, was made a scapegoat for the Clinton administration, which was accused of turning a blind eye on the espionage scandal because it had received 1996 campaign contributions from Chinese officials. The FBI, in turn, expended vast sums of money to support their predetermined conclusions that Wen Ho Lee was a spy, the lawsuit charges.

The American Association for the Advancement of Science and the American Physical Society have both written letters to Janet Reno, protesting the inhumane conditions of Lee's confinement. The case, the groups warned, is already having an adverse impact on the ability of the weapons labs to recruit and retain scientists. "The extraordinarily harsh conditions under which he is detained suggest to the outside world that he is presumed guilty and is being punished before his trial has even begun," an American Physical Society representative wrote.

An assistant to Reno defended the conditions of Lee's confinement and noted that even the judge had agreed that his release posed a national threat because of "the risk that Dr. Lee will find a way to, and will be inclined to, reveal to unauthorized persons the location of the seven missing tapes or to assist an unauthorized possessor in understanding and utilizing the information contained in the tapes." Reno's aide also pointed out that Lee is getting more time to visit with his family than other prisoners who are similarly situated.

Numerous scientists familiar with nuclear weapons believe that Sandia's Paul Robinson, as well as the Los Alamos physicists, grossly overstated the harm that would occur if the tapes fell into the wrong hands: Building a workable nuclear weapon requires not just codes, but engineering skills and an adequate amount of plutonium or enriched uranium. In a letter to the Wall Street Journal, Harold Agnew, a former director of Los Alamos, wrote, "Being able to use information from any of the national laboratories' codes requires a great deal more knowledge than following a cake recipe...No nation would ever stockpile any device based on another nation's computer codes. Maybe for security reasons the originator has included a 'virus' that would result in a dud if the codes were to be followed exactly."

The Albuquerque Journal also pointed out recently that many of the files that Dr. Lee downloaded actually had a security designation known as "PARD," an acronym that stands for "Protected As Restricted Data." This is a category reserved for information that is technically considered classified but has not yet undergone the formal classification review process. PARD data, for example, might include printouts of mathematical calculations and could be left out on a scientist's desk in the secure area overnight.

Meanwhile, the government is moving ahead with trial preparations, which will be complicated enormously by the amount of classified material that must be handled. At the federal courthouse in Albuquerque, carpenters have just completed construction of a Secure Compartmented Information Facility, or SCIF. No electronic signals will be able to penetrate or escape from the specially enclosed facility. In this tomb-like room, away from the eyes of the jury and the media, prosecutors, defense lawyers and the judge will hash out disputes over what classified information can be declassified and admitted at trial. Chief U.S. District Judge John Conway, who will preside at the trial, recently ruled that the Classified Information Procedures Act, or CIPA, is constitutional and can be applied during the trial. That means that the defense team will have to identify beforehand what kind of classified evidence it plans to introduce in order to give the government the opportunity to first assess whether the information will damage national security and, if so, whether other information or substitutions can be used.

With the exception of the judge, everybody involved in the case -- from the bailiff to the court reporter to the secretaries, clerks and attorneys -- will need Q clearances. And the background checks do not come cheaply, notes lead prosecutor Robert Gorence. But Gorence, who has had to master physics and mathematics and computer science, adds, "There is nothing about this case that will be inexpensive."

Gabby Templet contributed to this story.


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