The main conflict in this story is between the Baskervilles and the curse that seemingly haunts them. The danger to Sir Henry from the scheming Stapleton is real enough. Holmes and Watson, of course, champion Sir Henry and so they are on the side of good against the evil represented by Stapleton.
Stapleton's hounding (if one may forgive the pun) of first Sir Charles Baskerville and then Sir Henry stems from a family conflict, as it turns out. Stapleton, being a distant cousin of Sir Henry, has his eye on securing the Baskerville estate for himself.
This conflict in this story takes on an interesting extra dimension: the opposition between rationalism and superstition. The hound inspires all the more fear as it is believed to be a demon - as elaborated by the lurid legend related by Dr Mortimer early in the story. Holmes therefore has to deal with not just the physical threat to the Baskerville heir, he also has to debunk all the fear surrounding the hound, and the gloomy desolate moor and the forbidding Grimpen Mire. His scientific rationalism triumphs in the end, so that he finally remark with some confidence that 'I do not know that this place contains any secret which we have not already fathomed' (chapter 14).