In The Hound of the Baskervilles, as in most detective mystery genre works, the brilliant detective must sift through many clues, some of which are red herrings, to solve the mystery. The Hound of the Baskervilles presents a twist on detective stories, since no crime has actually been committed. Sir Charles Baskerville died of natural causes and was not murdered per se, but his death forewarns Holmes of a crime in the works that must be prevented, namely the murder of Sir Charles's heir, Sir Henry.
The clues that Holmes uses to prevent Sir Henry's murder and to explain what frightened Sir Charles to death are given below along with their significance.
The dog footprints at the location of Sir Charles's death, the stolen and returned new boot of Sir Henry, and the stolen but not returned old boot of Sir Henry all signify that a real dog, not the mystical dog of the Baskerville curse, is involved in Sir Charles's death as well as the plot to take Sir Henry's life.
The written warning note to Sir Henry (which smells like perfume) and the warning that Miss Stapleton delivers to Watson when they meet implicate the Stapletons in the plot. The reaction of Mr. Stapleton to his "sister's" meeting Sir Henry on the moor is suspicious and is explained by the fact that the two Stapletons are only masquerading as siblings but are really married.
Barrymore gives Watson a note signed "LL" that requested a meeting with Sir Charles the night he died. Holmes finds out LL is Laura Lyons and interviews her while he leaves Watson to watch over events at Baskerville Hall. The relationship of Laura to Stapleton helps Holmes create the link between Stapleton and the Baskervilles. Holmes notices a resemblance between Sir Hugo Baskerville's portrait and Stapleton, which helps Holmes realize that Stapleton could be an heir plotting to get the Baskerville estate. Holmes also researches Stapleton's past, which helps him piece together what Stapleton is trying to do.
The biggest "clue" Holmes uses to solve the mystery is a risky one. He uses Sir Henry as bait, allowing him to leave the Stapletons' at night to walk home to Baskerville Hall, and Sir Henry is attacked by a dog painted with phosphorescent paint. Holmes shoots the dog, and Holmes and Watson rush back to the Stapletons' to find Mrs. Stapleton bound and gagged by her husband. She reveals to them her husband's plot and his hiding place on Grimpen Mire.
True to the form of a detective novel, Holmes explains all his reasoning and fills in the blanks in the final chapter of The Hound of the Baskervilles.