What was Holmes' theory about Sir Charles' death?

Holmes proposes two questions: 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.