Suddenly the winds have shifted. Wen Ho Lee is free, and the New York Times, which a year and a half ago all but convicted the Los Alamos scientist of passing the nation's most precious nuclear secrets to China, now excoriates the government for having gone after the wrong man.

On March 6, 1999, the Times headline read "Breach at Los Alamos: A Special Report; China Stole Nuclear Secrets for Bombs, U.S. Aides Say." The stolen bomb design referred to the W-88 warhead, the most advanced in the US nuclear arsenal. The Times's reporting was based on leaks from a Congressional committee headed by right-wing Republican Christopher Cox, who was determined to prove that campaign contributions to Clinton had corrupted national security. Lee was the fall guy, having been singled out by an Energy Department whistleblower, Notra Trulock, Cox's star witness and key Times source, whom critics inside and outside the department have accused of a pattern of racial profiling in affidavits.

The government was forced to exonerate Lee of any connection with the W-88 warhead. In order to save face and pacify Congressional critics and their allies in the media, prosecutors seized on their discovery of a minor transgression of laboratory rules: Lee had downloaded data from one machine to another and to tapes within the lab. But this was material he was authorized to work with. Also, the files were classified secret only after he had downloaded them, and the most knowledgeable experts in the field have testified that virtually all the information was already in the public domain. Nonetheless, the government hyped this material as the "crown jewels" of the nuclear arsenal, the media played along and Lee was indicted last December on fifty-nine counts, thirty-six of which carried a life sentence.

The material was judged by the government to be so sensitive that Lee has been held in a tiny jail cell in solitary confinement for nine months. The frail, 60-year-old scientist, who recently survived a bout with cancer, was shackled during his brief moments outside the cell, his diet was poor and his health deteriorated. Contact with family and attorneys was severely restricted. In early September, Lee was to be released on bail under stringent conditions of house arrest imposed by the judge, but prosecutors appealed the decision, leaving Lee to languish in jail.

Then suddenly on September 11 the same Justice Department prosecutors who had at one point threatened Lee with the electric chair, invoking the Rosenbergs, decided that Lee's freedom posed no danger. The government plea-bargained away fifty-eight of their fifty-nine counts to a single felony count of the improper "retention" of files. No spy, no stolen nuclear secrets, no scandal. Lee was free to go without probation or restrictions on travel. The government settled because its case was crumbling. The key FBI investigator admitted deceiving the judge on several points of testimony relating to Lee's honesty. The government also admitted lying to Lee, telling him he'd failed a lie detector test that he'd passed with flying colors.

And the federal judge, James Parker, who has viewed in camera much of the material incriminating the government on the racial profiling claim of the defense, had ordered the Justice and Energy departments to turn over thousands of pages of evidence relating to that claim. These factors further impelled the prosecutors to settle, but clearly not out of any sense of fairness. Justice prevailed, except for the deep wounding of a man forced to witness the destruction of his reputation and to suffer jail conditions that if applied to a scientist in a totalitarian country would have brought a flood of complaints from human rights organizations.

That did not happen in this case. Instead, it was left to Asian-American leaders to rally to Lee's defense. They cited historic precedents for the loyalty of Asian-Americans being questioned, which, incidentally, has led to a recruitment problem for the weapons labs. Impressive legal talent was provided pro bono by two Los Angeles lawyers, Mark Holscher, a conservative Republican and a partner in O'Melveny & Myers, and Brian Sun, whose own law firm volunteered many hours on behalf of the family.

But where was the rest of the human rights community in this modern equivalent of the Dreyfus case? Are we still, even after the demise of the cold war, so traumatized by national security arguments that we are afraid to speak up even in the face of the most absurd claims of spying?

Absurd on their face: China has a primitive nuclear force of about twenty liquid-fueled rockets, and it would take that country decades to mount even the slightest of credible threats to the United States, with its 6,000 warheads primed for instant retaliation. Do we still believe that there are nuclear secrets when scientists from the former Soviet Union are circling the globe with résumés in hand? Or was the relative silence in the Wen Ho Lee case due to a fear among progressives of visiting greater troubles upon the Clinton Administration amid the wild Republican charges of the Clinton/Gore China connection?

Whatever the cause of this silence, this is one of the most shameful episodes in the history of US jurisprudence and journalism. An entire community of loyal Americans was maligned, beginning with Lee, solely for their ethnic identity. Throughout, Janet Reno's Justice Department proved to be vindictive in the extreme and committed to the view that a Taiwanese-born-scientist-turned-US-citizen who has loyally worked for the security of this country most of his life must be judged guilty before trial.

An apology is owed Lee, who even in his moment of vindication was forced to admit guilt to a felony charge never leveled against anyone in a comparable situation. Former Director of Central Intelligence John Deutch, a case in point, downloaded top secret files (not unclassified ones, as did Lee) to his home computer, where they were easily accessible to hackers. But he's a member of the good-old-boy national-security club, and he has not been charged with anything. An investigation of this double standard of law enforcement is in order, and it must begin with the role of Reno and her Justice Department, which seemed all too eager to play the part of Grand Inquisitor.

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