Go to Baskerville Hall and ask Sir Henry HOLMES, then find Watson in town and ask him HELP, then go see Holmes in the ruined abbey on the moor. It's ESEESD of the twisted alder tree where the hound shows up at night. The entrance to the Abbey opens and closes, so it's possible that it won't be available when you try to go to Holmes at any point in this quest, and you'll have to wait for it to open again. Ask holmes HELP, and he suggests that Stapleton has been acting strangely. Ask holmes Stapleton and he suggests talking to him (and that beating him up will make him more cooperative). Attack stapleton, and he'll stop fighting you when he's low on health. He doesn't hit very hard.
Ask him BASKERVILLES and he tells you he's the rightful heir to Baskerville Hall. Ask him PROOF and he'll give you some papers, and tell you to show them to Bishop Graves. He'll also threaten to call the hound after you if you give them to Henry Baskerville.
Ask him HOUND and stapleton will tell you that the hound knows him and reacts to his whistle. He'll ask if you'll help him be rid of holmes. Say YES, he'll tell you he was planning to get the Hound to attack Holmes using the whistle, and tell you to go to Holmes and use the whistle. Ask him WHISTLE and he will give you the whistle (it's weird that he doesn't do this after he tells you his plan, but there you go). Saying NO doesn't seem to do anything, and you can still say that you'll help stapleton.
If you go back to Holmes and ask him Stapleton he'll tell you he's tracked the hound to the crypt. If you ask Holmes about the whistle (or give him the whistle), he tells you to go play it. If you play it at this point, the hound will come. It won't attack Holmes, it will most definitely attack you (and it will continue to not attack Holmes even if you flee out). This is a hard fight with a tough mob (for most people), AND if you're in the room with Holmes, Holmes will block healing, or at least surgery, so you'll have to flee out if you bring a healer. This doesn't actually appear to be a part of the quest, and when I killed the hound, Holmes didn't make any note of it!
If you give Holmes the documents, he looks them over and tells you to give them to Sir Henry Baskerville. At this point, you can give the documents to either Sir Henry or to Bishop Graves.
If you give them to Sir Henry, you'll get the whois ...helped the world's greatest detective solve his toughest case!
If you give them to Bishop Graves, you'll get the whois ...helped enshroud evidence of a murder mystery!
As a special note to the careful reader, who has read all of this before jumping into the quest, note that you can ask Stapleton PROOF twice at that part of the quest, and get two sets of documents and both whoises (give the papers to Bishop Graves first, then to Sir Henry for both - Verified 05/04/2019).