Neil Gaiman calls his "A Study in Emerald"* a Lovecraft/Sherlock Holmes fanfiction. And indeed it is exactly that: it uses the narration and story structure pretty characteristic to one from Arthur Conan Doyle's stories about the famous detective. The difference is in the background: in this story, the Cthulhu Mythos Creatures live happily among us... mostly as nobility, which is happy to devour body, mind or soul of any commoner.
In the story, the narrator returns from the war in Afghanistan and finds a room with an eccentric genius living at Baker Street. Soon, they are approached by Scotland Yard to help solving the murder of a German prince, whose green blood has been splattered over the walls.
The antagonists are apparently a doctor and an actor who enjoys changing his appearance.
So my question is - if we assume that this is indeed the world of Arthur Conan Doyle - who is who from the "Sherlock Holmes" universe? Is it (as in the original) Holmes and Watson chasing Moriarty and his cronies, even if they've committed murder to protect humanity? Or is it other way around - Holmes and Watson are the outlaws being pursued by the law-abiding Moriarty?