Sounds like he was most likely involved in some serious shit that was off the books and somehow it came to light. His boss is probably aware of what it was but no one will admit shit. It went awry and he is left holding the bag.
Gold and money for an operation that could have been to anything from funding armed rebellion to god only knows.
$40m+ in an expense account based in gold bars is absolutely crazy. CIA agents must have access to untold resources if this is seen as a somewhat regular 4 month spend. Seems it is, given that they seemingly weren't concerned about the $40+ million being taken out, but where it was being held.
I'm imagining its like the Continental Hotel in John Wick. Everything you need to fund and arm an insurgency, checking it out from facilities like I might with an AV adapter.
Or, someone decided they wanted to redirect the flow of black money through someone else, but couldn't do it internally for some reason; so they called in their FBI friends to make a ruckus. While the guy is busy defending himself, they have an excuse to pick someone else to receive the new stream of gold.
Gold and money for an operation that could have been to anything from funding armed rebellion to god only knows.