Confusion about the cowl can early on be that descriptions of cloaked figure in black around during murders/vanishings may make a listener think the figure in black hood that is behind new criminal network. Later finidng it was skaven, were the skaven using humans? (instead of the truth, a human using skaven).
You can develop the criminal group more, I'm calling it the Brotherhood, and it can have some minor crime bosses who become part of it. They all wear black hoods, it's an organization that has a "cell structure" with individual bosses that seldom meet. Any of these bosses may seem to be the "black cowl". There may be a "day to day" boss who thinks they are the real power merely taking "advice" from a helpful supporter who only wants a cut of the take (the real black cowl) and is your patsy. The whole "black cowl" thing can be a red herring - the main villain with the template card can just be the "conspirator" behind the "black dowl patsy".
You can even let them think they have defeated the criminal in Part 1 and Part 2 is carrying them on to clean up the artefact. This works just fine.
I'm also toying with the idea that the Black Cowl wears is a magical artefact that, among other things, disguises his voice.
And, last but not least, if you're really evil - there isn't just one Black Cowl. If one falls, the Conspiracy and the Great Conspirator will raise up another.
Another option is to make whichever one you would choose only "think they are the prime mover" and really it's their lieutenant figure in each case who is the real power.