Holmes, excited by such a mysterious case, asks for more details. As it turns out, the paw prints indicated that the dog had not approached the body. High hedges and two locked gates bordered the Yew Alley. Mortimer suggests that the death was the result of some supernatural evil, and he describes his own interviews with locals, who had seen a spectral hound roaming the moors. The superstitious Mortimer only came to Holmes to ask what to do with Sir Henry, the sole heir, set to arrive at Waterloo Station in one hour. He mentions another heir, Sir Charles's brother Roger, but points out that he is presumed dead in South America. As for Sir Henry, Mortimer is afraid should he set up shop in Devonshire, but he knows that the county is counting on continued Baskerville philanthropy.
Holmes promises to consider the matter, telling Mortimer to pick up Henry at the station and bring him to the office the next morning. The detective dismisses Mortimer and Watson and settles down to contemplate the situation, ruminating in his typical fashion over a bag of Bradley's strongest shag tobacco.
Later that night, Watson returns to find the office atmosphere thick with smoke: as Holmes suggests, "a concentrated atmosphere helps a concentration of thought." Holmes surprises Watson by guessing he has been at his club and unveils a map of the Baskerville moorlands. Holmes indicates his inclination to go through all the other possibilities before falling back on the supernatural one, and he speculates on the relevant questions. Given his infirmity and fear of the moor, Holmes wonders whom Charles was waiting for at the gate. The change in footprints, Holmes suggests, indicates running and not tiptoeing. Holmes also points out that Sir Charles was running in exactly the wrong direction—away from his house and any help he might find. The duo sets aside the case and Holmes takes up his violin.
The next morning, Mortimer and the young Henry Baskerville arrive at 221b Baker Street. Though sturdy and weather-beaten, Sir Henry's expression showed that he was a gentleman. Just twenty-four hours in London, Sir Henry has already gotten involved in the mystery—he received an anonymous note of warning when he arrived at his hotel. Said the note: "As you value your life, or your reason, keep away from the moor." A few facts stand out: the address is on a plain envelope and printed in rough writing, and the note itself is composed with words cut out of a newspaper, except for the word moor. Holmes establishes that no one could have known where to reach Sir Henry, so the writer must be following him. Holmes quickly assesses the typeface and discerns that the words were cut out from yesterday's Times. He goes on to suggest that the culprit used a pair of short-bladed nail scissors, since the longer words are cut with two snips, and that the word moor was handwritten because the author could not find it in print.
Astounded, the others listen on intently. Holmes proceeds: the author must be an educated man, since only the well-educated read the Times. As such, the roughly written address suggests the writer was trying to disguise his or her handwriting, thus, the writer must have cursive that is recognizable. In addition, the author must have been in a hurry, since the words are glued carelessly onto the paper.
Dr. Mortimer, suddenly skeptical, questions Holmes' guess work, and the Holmes retorts that his methodology involves weighing probabilities and deciding on the likeliest solution. To prove it, he points out that the spluttered writing suggests a lack of ink, undoubtedly the result of a hotel pen, and not a private one. Holmes even asserts that an investigation of hotel garbage around Charing Cross, where the letter was postmarked, should yield the torn-up copy of the Times.
Announcing that he cannot glean anything else from the letter, the detective asks Henry whether anything else unusual has happened. Apparently, when Henry put a new pair out to be shined, his boot was lost or stolen. Dismissing the incident, Holmes agrees to fill Henry in on the curse of the Baskervilles. The group debates whether the warning suggests a friend eager to protect the baronet or an enemy intent on scaring him off. Henry announces his intention to go to Baskerville Hall. After inviting the detectives to lunch later that day, he leaves.
As soon as Sir Henry and Mortimer are out the door, Holmes leaps into action, intent on trailing the baronet to spot the letter writer whom Holmes suspects is trailing Sir Henry. Sure enough, the stakeout reveals a suspicious stranger in a cab, but the moment Watson spies his bushy black beard, the villain hurries off. The spy, Holmes suggests, is a worthy rival given his choice of a cab, a supremely well-suited getaway car. Holmes own performance, by contrast, was sub- par: he let the spy know that he was seen. The detective does announce that he has caught the cab's number, 2704, and directs Watson into a nearby messenger office. Once inside, Holmes greets the manager, a former client, and asks for the man's son Cartwright's help. Holmes instructs Cartwright to inspect the garbage of all the hotels in the Charing Cross region, in search of the mutilated Times. Meanwhile, he tells Watson, they will investigate cab number 2704 before meeting Sir Henry for lunch.
In this section, Holmes attacks the case, applying his logical methods to the few clues that they have. His decision to exhaust all real-world options before considering the supernatural is typical of Holmes' style. He decides to rule out all possibilities before he considers that there are supernatural reasons. Ironically, the way that he analyzes clues, and the intuition he uses to gather evidence, is almost supernatural. He is almost superhuman in his keen powers of observation. The book has a very mysterious and dark undertone. These two chapters introduce us to some of the more puzzling clues in the book—the cut-and-paste warning letter, the stolen boot, and the mysterious stranger. In particular, the appearance of the mysterious stranger highlights one of the more prevalent themes in the story: disguised identity. When the detectives spot their man, they cannot help but wonder whether the black beard is a fake. The man's hurried escape ensures that for now, they will not figure out his identity, or whether the beard is a disguise. At the same time, identities and intentions get confused as the detectives wonder whether the stranger and the letter writer are the same person, and whether that person is a friend or an enemy. In this case, a mistaken or uncertain identity adds to the building tension and the tone of mystery in the novel.
Mistaken and disguised identities play a large role in the novel. The villain will continually disguise his own and others' identities. Just like an episode of Scooby Doo, the buildup to the final unmasking, or the revelation of true identities, creates much of the suspense in the story. The conflict between an inexplicable, mysterious, or supernatural identity and a more realistic and logical one, drives the plot of the novel. These two sides: practical and supernatural also represent the different characters' perspectives about Baskerville mystery. Holmes takes a more dogmatic, methodological approach, whereas Mortimer believes in the supernatural explanations.
These chapters also introduce us to the character of Cartwright. Cartwright offers an interesting glimpse into the mindset of upper middle class England during Holmes' time. As an educated person, Holmes expects not only respect, but also service from his social inferiors, and he usually gets it. Cartwright agrees to go rummaging about in the trash for Holmes. Later on, when Holmes and Watson handle an irate cab driver, a few shillings buys him off and ensures his total cooperation. The detectives' interaction with people of lower classes suggests that they do not respect those people whom they consider of a lower social or economic status.