The mysterious workings of a Pentagon office that oversees clandestine operations are unraveling in federal court, where a criminal investigation has exposed a secret weapons program ... to manufacture an untraceable batch of automatic-rifle silencers. The silencers - 349 of them - were ordered by a little-known Navy intelligence office at the Pentagon known as the Directorate for Plans, Policy, Oversight and Integration. The directorate is composed of fewer than 10 civilian employees, most of them retired military personnel. Court records filed by prosecutors allege that the Navy paid the auto mechanic - the brother of the directorate's boss - $1.6 million for the silencers, even though they cost only $10,000 in parts and labor to manufacture. If the foreign-made weapons were equipped with unmarked silencers, the source said, the weapons could have been used by U.S. or foreign forces for special operations in other countries without any risk that they would be traced back to the United States. No documentation has surfaced in court to indicate that Navy officials formally signed off on the silencer project, although many pretrial motions have been filed under seal. Hall, the directorate official charged with illegally purchasing the silencers, has asserted that he received verbal approval for the secret program from Robert C. Martinage, a former acting undersecretary of the Navy, according to statements made during pretrial hearings. Martinage was forced to resign in January after investigators looking into the silencer deal found evidence that he had engaged in personal misconduct ... unrelated to the silencer contract.