THE SERIOUSNESS of the charges filed against Wen Ho Lee last week adds an additional layer of confusion to the already murky Chinese nuclear espionage scandal. Mr. Lee, the scientist fired from the Los Alamos National Laboratory, was initially suspected of passing information on the W-88 warhead to the Chinese. The FBI, however, was ultimately unable to substantiate this allegation, and the bureau has since expanded its search for the W-88 spy beyond Mr. Lee and Los Alamos. In the process of investigating Mr. Lee, however, the government found evidence that he had mishandled classified information by downloading it onto his unclassified computer. And the wide expectation was that Mr. Lee would be prosecuted not for espionage but for these comparatively minor security breaches.

The indictment that came down on last week, however, alleges far more than simple security infractions. The government did not charge Mr. Lee with spying; in fact, the U.S. attorney who brought the case--John Kelly of New Mexico--specifically stated that the government does not allege "that Lee passed classified information to any particular foreign government, including the People's Republic of China." At the same time, the charges suggest far more than mere carelessness. Many of the 59 counts against Mr. Lee charge that--in assembling sensitive weapons information, downloading it to unclassified systems and then copying it onto portable tapes--he acted "with intent to injure the United States and with intent to secure an advantage to a foreign nation." The combination of these intent allegations and the disturbing fact that most of the tapes in question have not been recovered suggests that the government believes worse of Mr. Lee than prosecutors are prepared to allege in court.

Mr. Lee is, of course, innocent until proven guilty--a presumption that he has been largely denied in the public arena throughout much of the investigation. But the seriousness of the allegations against him should give pause to those convinced in advance of Mr. Lee's innocence, just as surely as the shifting nature of the allegations against him should give pause to those convinced he is a nuclear spy. Given the poor handling of this investigation to date, it is well worth reserving judgment until the government proves the very grave accusations it has now leveled.