The silencers – 349 of them – were ordered by a little-known US Navy intelligence office at the Pentagon called the Directorate for Plans, Policy, Oversight and Integration, charging documents show. The directorate is made up of fewer than 10 civilian employees, most of them retired military personnel. Court records filed by prosecutors allege that the US Navy paid the mechanic – the brother of the directorate's boss – $US1.6 million ($1.83 million) for the silencers, even though they cost only $US10,000 in parts and labour to manufacture. Much of the documentation in the investigation has been filed under seal on national security grounds. The records that have been made public show the crux of the case is whether the silencers were properly purchased for an authorised secret mission or were assembled for a rogue operation. A former senior navy official familiar with the investigation described directorate officials as "wanna-be spook-cops".

Speaking on the condition of anonymity, he said: "I know it sounds goofy, but it was like they were building their own mini law enforcement and intelligence agency." The directorate is a civilian-run office that is supposed to provide back-office support and oversight for US Navy and Marine intelligence operations. However, some of its activities have fallen into a grey area, crossing into more active involvement with secret missions, a former senior Defence Department official says. "By design, that office is supposed to do a little more than policy and programmatic oversight," the former defence official said. "But something happened and it lost its way. It became a case of the fox guarding the henhouse, and I suspect deeper issues might be in play." Navy officials declined to comment, citing the ongoing investigation and prosecution.

Prosecutors have said that the silencers were acquired for a "special access program", or a highly secretive military operation. A contracting document filed with the court states that the silencers were needed to support a program code-named UPSTAIRS but gave no other details. In court papers filed by prosecutors, one directorate official told an unnamed witness that the silencers were intended for Navy SEAL Team 6, the elite commando unit that killed Osama bin Laden. But representatives for SEAL Team 6 told federal investigators they had not ordered the silencers and did not know anything about them, the court papers show. Sorting out the truth has been made more difficult by the elimination of potential evidence.

At one pretrial hearing, a defence attorney for the mechanic, Mark Landersman of Temecula, California, accused the navy of impeding the investigation by destroying a secret stash of automatic rifles that the silencers were designed to fit. Prosecutors immediately objected to further discussion in open court, calling the matter classified. The destroyed weapons were part of a stockpile of about 1600 AK-47-style rifles that the US military collected overseas and stored in a warehouse in Pennsylvania, a source familiar with the investigation said. If the foreign-made weapons were equipped with unmarked silencers, the source said, the weapons could have been used by US or foreign forces for special operations in other countries without any risk that they would be traced back to the United States. A different source, a current senior navy official, confirmed that an arsenal of AK-47-style rifles in a warehouse in Pennsylvania had been destroyed within the past year.

But that official suggested the issue was a smokescreen, saying that the weapons were being kept for a different purpose and that no program had existed to equip them with silencers. In a separate move that eliminated more potential evidence, US Navy security officers incinerated documents last year that they had seized from the directorate's offices in the Pentagon, court records and testimony show. Two navy security officers have testified that they stuffed the papers into burn bags and destroyed them on November 15, 2013; three days after The Washington Post published a front-page article about the unfolding federal investigation into the silencers. One of the security officers said it did not occur to her that the documents should be preserved, despite navy policies prohibiting the destruction of records that could be relevant to lawsuits or criminal investigations. The officer, Francine Cox, acknowledged that she was aware the navy directorate was under scrutiny and that she had read the Post article shortly before burning the documents.

But she said she did not think the papers were important. "I didn't think the information we had was pertinent," she testified at a pretrial hearing in July. "If you don't tell me to hold on to something, I don't have to hold on to it." Lee Hall, a navy intelligence official who is charged with illegally purchasing the silencers and whose trial is scheduled to begin this month, argued that the burnt material was crucial to his defence. He said the documents included handwritten notes and other papers showing the undersecretary of the navy at the time had authorised the project. "My notes would show I acted in good faith," Mr Hall testified at the July hearing.

Stuart Sears, an attorney for Mr Hall, declined to comment. US District Judge Leonie Brinkema rejected a bid by Mr Hall's attorneys to dismiss the charges against him but was incredulous that the navy had destroyed the documents. "I don't find any nefarious evidence, or evidence of bad intent, but it sure does look to the court like negligence," she said. On other occasions over the past year, Judge Brinkema has questioned whether prosecutors were fully aware of what the navy directorate was up to and whether they really wanted to expose its activities by taking the case to trial. "We're getting deeper and deeper into a morass," she said at a hearing in March. "One of the things the government always has to think about is the cost-benefit analysis. At the end of the day, is this particular criminal prosecution worth the risk of having to disclose or reveal very sensitive information?"

Washington Post