Deception
There is a great deal of deception in this work, starting with Porlock and Moriarty. The central deception, of course, is John Douglas, who is actually McMurdo, who is actually Birdy Edwards. Edwards deceives all of the Scowrers as well as Ettie initially; then in England he deceives Cecil and his wife. The deception deepens with his faked death, but even then it is not enough to fool Moriarty (or Holmes, of course). Deception is used for both moral and immoral reasons. Moriarty deceives to gain power; Edwards deceives in order to gain access to a society of murderers whom he seeks to bring down. Doyle suggests that deception may be useful but that one has to be very careful to not lose himself within the disguise.
Authority
Sherlock Holmes possesses a great deal of authority through intellect, capability, and efficiency. The other characters in this work, primarily the Scowrers, possess authority through more deleterious means: they threaten, terrorize, wound, kill, and seek to establish their authority on the basis of being able to do all of these things without retribution. Authority within the organization is not based on sound ideas or intellect; rather, it is established and maintained by force. Doyle suggests that this sort of authority is doomed to fail eventually because it is not sustainable.
Power
Power manifests itself in many ways in the text, but Doyle clearly seems to suggest that the type of power Sherlock Holmes possesses is ideal. This power is rooted in intellect, logical and deductive reasoning, thoughtfulness and care, perspicacity, openmindedness, and clarity of thought and expression. Holmes is able to solve the case through all of these traits, restoring Douglas to his wife, exonerating him from punishment, and, although ultimately failing, protecting him somewhat from the threat of Moriarty. Doyle explores other forms of power like traditional law enforcement, which he depicts as useful but limited, and power based in violence and terror, which he depicts as putatively absolute but ultimately doomed to fail.
Observation
One of the most important themes of the novel is observation, which is what readers are encouraged to practice along with Holmes. Doyle sets out the particulars of the case without sparing any details in order to prompt his readers to think about what they see and try to form connections. Holmes is incredibly smart, but all of the evidence he has is the same evidence that readers have at the beginning. Doyle teaches his readers to consider every detail no matter how small, to not let one's preconceptions take prominence, and to be openminded.
Faith
One of the most compelling parts of the Holmes stories is the relationship between Holmes and Watson. If this is the only Holmes story readers have ever read, then it still does an excellent job at portraying the relationship and demonstrating how both men benefit from it. Watson's faith in Holmes's abilities is ever-apparent here, as it is in other stories. Holmes's ideas occasionally seem wild or impossible, but Holmes always gives his friend credit. Watson's faith may be tested but it never falters; this is the recipe for not only a good friendship but also a dynamic detective duo.
Fear
The title of the novel suggests how much fear plays a role in the events depicted within. The "Valley of Fear" is both a physical place—Vermissa Valley, heart of the Pennsylvania coal mines—and a symbolic place. In the latter sense it is a psychological valley in which Douglas finds himself stuck with no means of escape. He is menaced and burdened by his fear and knows that he can never escape it. It permeates all aspects of his life. Ultimately, fear keeps Douglas on his toes and alive a lot longer than if he had been complacent, but it cannot fully save him.
Morality
On the one hand, Doyle is clear about morality within the story. The Scowrers are practically irredeemable, characterized by near-senseless violence. They tolerate no threat to their authority and menace innocent people. However, McMurdo poses a more interesting moral conundrum for readers. While he is undercover with the Scowrers, he beats, threatens, lies, and most likely kills people. He also watches and says nothing in many of these situations, though he does warn Wilcox and saves Stanger from being beaten to death. One wonders if he is just as bad as the Scowrers even though he eventually puts them away. It is perhaps easier to say that he is doing a good thing, but without knowing just how fully he participated in their bloody deeds, it is impossible to say so definitively.
