The Oxford English Dictionary says that “skulduggery” means underhand dealing, deceptive intrigue or machination and trickery. It gives several forms of the spelling. The OED even has it as a verb — to skuldug, and quotes William Faulkner using it in 1936.
This is an 18th century Scottish word, originally spelled “sculdudrie,” that refers to an indecent act, usually sexual and almost certainly was used to describe adultery.
The combination of “skull” and “duggery” (which sounds like an archaic form of “digging”) may remind one of the grave-robbing that was widespread in the 1700s. But the original and more common spelling is “skulduggery,” (with only one ‘l’) and the term actually has no connection to either skulls or digging.
The first recorded instance in the US appears to be from the Burlington Daily Hawk-Eye, in Iowa, 28 Aug. 1858: “…we see nothing else in the new move but a bit of political skulduggery for the benefit of black republicanism; but it will not redound to their benefit — it will return to plague the inventors of the plot.”
It’s likely that the word came to North America with Scots immigrants aboard the many ships that sailed to America, and was perhaps corrupted by the ears of those immigrants from other nations who misunderstood the Scottish accent. In any case, the spelling of words often changes over the years.
Today “skulduggery” is usually associated with cloak-and-dagger intelligence agencies, but freelancers and domestic political operatives have made good use of “skulduggery” on occasion. It was most famously used by the Times in 1980 when referencing Watergate.
Well, if skulduggery is most used in political theater, I guess I can’t apply it to my cat trying to con me out of my tuna sandwich.