As with many mystery or suspense novels, The Hound of the Baskervilles by Sir Arthur Conan Doyle portrays a conflict between good and evil, with the morally good characters trying either to avenge past wrongs or to prevent future ones, and coming into direct conflict with evil characters.
The major conflict which controls the overall arc of the plot is that between Stapleton and his rivals as heirs to the Baskerville estate. Although he succeeds in killing Sir Charles, due to the intervention of Dr. Mortimer and Sherlock Holmes, he fails to kill Sir Henry.
Many minor conflicts drive various subplots. Mrs. Stapleton eventually ends up in conflict with her husband because she objects to his murderous schemes.
Another subplot involves Selden, also known as the "Notting Hill Murderer" who has escaped prison. Mr. and Mrs. Barrymore are trying to help him emigrate even as the other locals and authorities are attempting to apprehend him.
Watson's efforts to identify the mysterious stranger (who turns out to be Holmes) make for a minor comic subplot, and a conflict that ends in a friendly discussion.
"The Hound of the Baskervilles" is the type of story in which the villain is not immediately identified but whose existence is inferable by the things he does. Sooner or later the identity of the criminal in a story like this has to be made known to the reader. The villain in "The Hound of the Baskervilles" is a man named Mr. Stapleton. He is described as follows in the eNotes study guide.
Mr. Stapleton [is] actually a rival heir who arranged the death of Sir Charles and plans the death of Sir Henry. He is a passionate entomologist and a fearless explorer of the Grimpen Mire, where he keeps the great hound. When he prepares to loose it on a victim, he coats it with phosphorous, which makes the animal glow and appear to breathe fire. In order better to entice Sir Henry, he insists that his wife pretend to be his sister. He dies in the Mire, fleeing from Holmes, Watson, and Inspector Lestrade.
Watson, acting as Sherlock Holmes' agent, meets Stapleton early in the story but does not suspect him of being, in effect, the true initiator of the conflict. Sherlock Holmes is the opponent because he is asked to protect Sir Henry Baskerville and perhaps to find out who was responsible for the death of Sir Charles Baskerville. Stapleton wants Sir Charles dead, Holmes wants him alive. This is the basic conflict. Watson has an unusually important role in this story, while Holmes remains in the background. Here is a situation in which both principals in the conflict are "offstage," so to speak, most of the time. The whole problem is to discover the identity of the perpetrator, the person who is causing all the trouble. Once Stapleton's identity is known, the story is about over. In a story of this type, the villain cannot remain unknown from beginning to end. Typically something occurs to remind the reader that this evil character is still at large and still dangerous, still motivated by whatever it is that motivates him.
There are many "serial killer" stories in the movies and on television in which the perpetrator is unknown and virtually invisible. Typically he kills someone, usually a woman. A detective is brought in to solve the murder and prevent future occurrences. Then another woman is murdered with the same modus operandi (M.O.). Still the cunning, elusive perpetrator is unknown and invisible. The detective sets a trap. The perpetrator is almost caught--almost! But he gets away. However, he leaves some clue. Finally the detective catches him and reveals his identity. It may turn out that he is someone known to the viewer--another detective, perhaps.
In "The Hound of the Baskervilles" the need to remind the reader of the unidentified villain's presence and persistent threat is met by having the fugitive named Selden, who is known as the Notting Hill Murderer, killed by the hound because Selden is wearing the discarded clothes of Sir Henry Baskerville, whose servants, the Barrymores, gave them to Selden. Naturally the hound takes Selden for Sir Henry. This is further proof that some unknown schemer wants to murder Sir Henry by setting a vicious hound on him. Holmes sets a trap and catches Stapleton who dies horribly in the mire while attempting to flee. The basic conflict may be a little hard to see because the cunning evildoer is unknown until late in the story.
There is a similarity between the plot of "The Hound of the Baskervilles" and that of "The Adventure of the Speckled Band." In the latter story Holmes is trying to protect Helen Stoner from an unknown person who murdered her sister Julia two years earlier. In "The Hound of the Baskervilles," Holmes is trying to protect Sir Henry from whoever murdered Sir Charles Baskerville.