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.
I thought this was baseless speculation, but from TFA:
> [he] asked for, and received, “a significant quantity of foreign currency and tens of millions of dollars in gold bars for work-related expenses.
$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.