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After Dr. Mortimer leaves, Watson leaves Holmes alone to think. When Watson returns later, he finds the room filled with tobacco smoke. With little effort, Holmes perceives that Watson has spent all day at his club. He then shows Watson a map which he has obtained of the moor, and points out the various locations mentioned by both Dr. Mortimer and the manuscript author.
Holmes proposes that there are two questions before them: first, has any crime been committed at all? And second, what is the crime and how was it committed?
Watson finds the case bewildering; Holmes agrees that it has a "character of its own" (164). He believes the tip-toe footprints are signs that Sir Charles was running, though he does not know what the man was fleeing. The fact that he ran away from the house rather than towards it suggests he was terrified out of his wits. Holmes also believes that Sir Charles must have been waiting outside for someone, which would explain the cigar ash that Dr. Mortimer described.