Lee accepted the plea, to one felony count of violating national security. Federal District Court Judge James Parker issued the apology and the rebuke.

To Lee, he said: As ``a member of the third branch of the U.S. government, the judiciary, the courts, I sincerely apologize to you . . . for the unfair manner you were held in custody.''

Of top officials of the Department of Justice and the Department of Energy, who were not in court, Parker said, their actions ``have embarrassed our entire nation and each of us who is a citizen of it.''

Parker's comments brought a discreditable trial to a fitting end, and offered some solace to Lee, his family and supporters for his 278 days in solitary confinement. Lee left the court with a felony conviction, but it was clear, from Parker's words, that the government bears shame for his treatment.

The government had targeted Lee, a Taiwan-born employee at the Los Alamos nuclear weapons lab, as the one it suspected of giving away advanced nuclear weapons secrets to China. But it never had any evidence that he committed espionage or that he gave away secrets to China or any nation. Nonetheless, even as its case fell apart, it relentlessly pursued charges that, if they had resulted in conviction, could have led to life imprisonment.

Lee ended up pleading guilty to the unauthorized downloading of nuclear weapons data from a secure computer to an insecure computer -- a violation that Lee has never disputed. In the plea agreement, the government acknowledges Lee's assertion all along that he never intended to harm the United States.

Parker had prodded the government to settle what he recognized was a weak case against Lee. In approving the agreement, Parker implied that more information damaging to the prosecution would have come out in a trial. Lee's lawyers would have presented testimony that Lee had been targeted solely because of his race.

Lee's nightmare is over, but the end of the case should not be the final word. Lee's indictment coincided with a maelstrom over relations with China. Parker's remarkable criticism of the higher-ups at Energy and Justice demands a congressional inquiry into who decided Lee should be prosecuted zealously -- and why. Sen. Arlen Specter, a Pennsylvania Republican, for one, has promised hearings.

A full accounting is vital as a check against future abuses of power.