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WaPo |  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 entwined with allegations of a sweetheart contract, fake badges and trails of destroyed evidence.

Capping an investigation that began almost two years ago, separate trials are scheduled this month in U.S. District Court in Alexandria, Va., for a civilian Navy intelligence official and a hot-rod auto mechanic from California who prosecutors allege conspired to manufacture an untraceable batch of automatic-rifle silencers.

The exact purpose of the silencers remains hazy, but court filings and pretrial testimony suggest they were part of a top-secret operation that would help arm guerrillas or commandos overseas.

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, according to charging documents. 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.

Much of the documentation in the investigation has been filed under seal on national security grounds. According to the records that have been made public, the crux of the case is whether the silencers were properly purchased for an authorized secret mission or were assembled for a rogue operation.