He flashed a wan smile and a timid wave to his friends and supporters when he first appeared in court, clutching a large brown mailing pouch stuffed with documents. But his placid face showed little else as former colleagues took the witness stand to denounce his deceptive behavior.

And when U.S. marshals finally led him back to solitary confinement last Wednesday, Wen Ho Lee showed no emotion, deepening the mystery of this once obscure nuclear weapons scientist whom government prosecutors now call an "unprecedented" threat to national security.

Why did he copy enough computer data to design a nuclear warhead when he didn't need all that information for his work? Why did he transfer top-secret computer codes to unsecure tapes? What happened to seven of the tapes? And if Lee destroyed them--as he claims--how, when and where did he do it?

Lee and his attorneys answered none of those questions last week as they tried unsuccessfully to persuade U.S. District Judge James A. Parker to release Lee on bail while he awaits trial for allegedly mishandling classified information, a felony charge that could put the 60-year-old scientist in prison for life.

Parker cited the lingering questions as he ruled, after three days of testimony, that no combination of bail restrictions could protect the country from the possibility that Lee might somehow pass the missing tapes to a foreign power.

And so the year of Wen Ho Lee ended much as it began, with government officials again calling the former physicist at Los Alamos National Laboratory a potential spy. Only now it is clear that Lee's alleged offense--downloading enough top-secret data to "change the world's strategic balance," as one expert testified--is potentially far more serious than the alleged theft by China of some information about the design of the W-88 warhead.

That is where it all began last March, when government officials fired Lee from his job at Los Alamos and identified him as their prime espionage suspect in an investigation into how China apparently obtained a few scraps of classified data about the W-88, America's most sophisticated nuclear weapon.

The espionage probe ignited a political furor in Washington, triggered a reorganization of the Department of Energy and dominated the Sunday morning talk shows for weeks last spring. But the case was murky from the start; some observers pilloried Lee as the most dangerous atomic spy since Ethel and Julius Rosenberg, while others called him a victim of spy hysteria on the part of China bashers.

When government officials first identified Lee as a suspect in the W-88 case, they knew nothing of his computer downloading, which was discovered only after Lee was fired and his office searched.

Federal officials acknowledged in April and May that they had no evidence to show that Lee spied for a foreign country, even as they launched the largest computer investigation in FBI history and weighed criminal charges against Lee for the downloading.

While all this was underway, a House select committee chaired by Rep. Christopher Cox (R-Calif.) made the espionage probe a cause celebre, only to have the President's Foreign Intelligence Advisory Board lambast the FBI and Department of Energy for prematurely focusing on Lee as the source of the W-88 leak. Other congressional committees reached similar conclusions.

By late summer, it even appeared for a time that Lee might avoid criminal prosecution altogether, as Los Alamos's former head of counterintelligence and two other officials involved in the investigation accused the government of singling out Lee as a suspect on the basis of his Chinese ethnicity.

But even after the FBI announced that it was going back to square one in the W-88 investigation and its agents expanded the probe beyond Lee and Los Alamos, he remained the focus of an investigation aimed at finding the missing tapes.

Lee was indicted Dec. 10 on 59 felony counts of mishandling 806 megabytes of computer codes and databases. This is the equivalent of more than 800,000 pages, a virtual catalogue of the nation's entire nuclear weapons program.

His colleagues expressed astonishment in testimony last week that any scientist with a top secret Q clearance could have committed so grievous an offense. They left no doubt that they too were mystified about why Lee lied to colleagues and methodically assembled all the know-how a foreign power would need to build nuclear warheads.

Government prosecutors, equally in the dark about Lee's motives, professed no such surprise at what they called his "surreptitious" and "nefarious" conduct. With FBI special agent Robert A. Messemer on the witness stand, they set out to document a "pattern of deception" by Lee stretching to 1982, when he telephoned a fellow scientist at Lawrence Livermore National Laboratory who was then under investigation for espionage and offered his assistance.

Questioned by the FBI, Lee initially denied knowing the other scientist and admitted making the call only after FBI agents told him they had it on tape. That pattern continued, Messemer testified, after Lee traveled on Los Alamos business to Beijing in 1986 and 1988 and filed false trip reports on his return. It wasn't until Lee took a polygraph test 10 years later, in December 1998, that he admitted having a clandestine meeting in a hotel room with a Chinese official during his 1988 trip, Messemer testified.

And it wasn't until a February 1999 polygraph indicated that Lee was being deceptive, Messemer told the court, that Lee admitted helping Chinese nuclear weapons scientists to solve specific problems during his 1986 and 1988 trips.

When Lee was asked in a March 5, 1999, FBI interrogation whether he had ever received correspondence from Zheng Shaoteng, Messemer said, Lee responded that he had received only a Christmas card from the head of China's Institute of Applied Physics and Conceptual Mathematics.

But when FBI agents searched Lee's home outside Los Alamos in April, Messemer said, they found a letter in Lee's garage from Zheng requesting that Lee send him some unclassified information from Los Alamos. "Doctor Lee, in his assertions to the FBI, has made a number of misleading or false assertions," Messemer said.

Each time that Lee transferred nuclear secrets from secure to unsecure computer systems, he lied to the Los Alamos computer by typing in that the files he was transferring were unclassified, according to testimony from Messemer and several Los Alamos officials. And to copy the unlawfully downloaded files onto even less secure portable computer tapes, they said, Lee lied to a colleague, saying that he wanted to copy a resume.

A hint of Lee's likely defense emerged as his attorneys aggressively cross-examined Messemer and the Los Alamos officials, asserting that their client failed to take a number of obvious steps that would have been expected from someone seeking to cover his tracks.

He failed to change file names, left classified data sitting on his unsecure office computer for six years, even called the help desk at Los Alamos's computer center in February and asked for instructions on deleting files.

John Cline, one of Lee's attorneys, established during cross-examination that Lee deleted large quantities of classified data from his unsecure computer and erased classified material from two portable tapes in early 1999 after it became clear that he was under investigation for espionage and about to lose his Q clearance.

While prosecutors cited these deletions as attempts by Lee to cover his tracks, Cline argued that they were part of a pattern by Lee to expunge classified material from his files because he soon would no longer be authorized to work with it.

Cline also sought to show that the material downloaded by Lee was related to his work; that scientists with Q clearances were permitted to put classified material onto portable tapes (though not in the way Lee did); and that there were no explicit rules prohibiting the destruction of tapes containing classified information.

At one point, Cline hinted at what might be called the "pack-rat defense," asking a Los Alamos official: "Did you ever conclude that Doctor Lee had a penchant for keeping things?"

Back in the courtroom gallery, among Lee's friends and supporters, the pack-rat defense was often mentioned as a possible explanation. "He had a wonderful collection of codes and code manuals," said Don Marshall, Lee's next-door neighbor, fellow weapons scientist and staunch defender.

Chris Mechels, a former employee of the top-secret X Division at Los Alamos where Lee worked, added that Lee's copying of computer files took place in 1993 and 1994, when the national laboratory was making a chaotic transition between computer networks and more than a few scientists were worried about losing files.

Mechels also noted that Lee's downloading took place shortly after he received notice that he might be laid off and could have represented an attempt to maintain access to his life's work. While that wouldn't make the downloading proper, Mechels conceded, it provides at least a plausible rationale for his actions.

But all these theories, coupled with the pattern of deception alleged by prosecutors, only complicate the puzzle. Even Marshall was perplexed by Lee's activities and his misstatements to authorities. "It is troublesome," Marshall said. "It would be nice to hear [Lee] comment on it."

In the end, Lee's lawyers argued that he deserved to be freed on bail because the government had no proof that he had ever disclosed, or planned to disclose, any of the secret data to a foreign country. But prosecutors countered that it was Lee who failed to show proof of having destroyed the tapes.

And if this were not mystery enough, Scott Larson, an FBI computer security expert, testified that there is no way to know whether a foreign intelligence service or sophisticated hacker broke into Lee's unsecure computer and read any of the classified files.

Such an intrusion is possible, experts said, because Lee's computer password and user name are known to have moved across the Internet in plain text and could have been stolen with relative ease.

"We don't know whether someone came in and took it all?" asked prosecutor Robert Gorence.

"That's correct," Larson said.

AT A GLANCE: Wen Ho Lee Case

MARCH, 1999: A Taiwan-born scientist at Los Alamos National Laboratory, Wen Ho Lee is fired for security violations. He had been under investigation since 1996 in connection with the 1980s theft of W-88 warhead information.

APRIL: After learning that Lee had transferred top-secret nuclear codes to his unsecured computer, the Energy Department shuts down computer systems at all its weapons labs because of concerns about possible espionage.

MAY: Secretary Bill Richardson announces an overhaul of security and counterintelligence activities at the Energy Department, including creation of a "security czar."

A House select committee issues a 700-page report saying China had obtained nuclear secrets about all U.S. warheads through a 20-year campaign of espionage.

DEC. 10: After hearing evidence for several months, a grand jury in Albuquerque issues a 59-count indictment accusing Lee of removing nuclear secrets from a secured Los Alamos computer. Lee is arrested and pleads not guilty.

SOURCE: Associated Press