This wasn't going the way I expected -- although I guess one of the standard detective plots involves the PI suddenly finding himself cast as the prime suspect.
I pointed out that equipment had been disappearing for months before I came on board, reminded him that his security detail was experiencing multiple alarms on a secure door without reporting it, and looked over at my boss for some support. The best I got was a meek assertion that he didn't believe I was a crook, but he didn't want me accusing other people without evidence. Finally, they asked me to the leave the room so they could "discuss options."
My boss never mentioned the subject to me again, even when I submitted a backdated spreadsheet of shortfall items averaging about US$3,000 a month. The thefts slowed during the next few weeks, but they never stopped. Then I was reassigned; the position of inventory clerk passed to a co-worker. I showed him my shortfall spreadsheet, as well as all the data I'd collected, and suggested he keep them updated.
I also passed along a proverb that would make a good title for a detective story, in which the hard-boiled investigator discovers a pattern of corruption starting right at the top: A fish rots from the head.