Rivalry
Rivalry plays a small, but fairly significant role in the events of The Whispering Skull. At the start of the novel, Lockwood and Co. make a bet with their rival agency, called the Fittes agency. Their chance says that whatever agency loses will need to publicly admit defeat in the newspaper, something which neither agency wants to do. However, after not having a case for many months, both agencies agree to the bet and their rivalry begins. Lockwood and Co. want to be the best agency and successfully solve as many cases as possible; Fittes agency wants the same. And throughout the book, they engage in a potent and often tense rivalry in which each would do anything they can to win the bet.
The supernatural
In all of the novels in Stroud's "Lockwood and Co." book series, the supernatural play an important role in the lives of the characters and the events in the novel. The supernatural—including ghosts, spirits, ghouls, and other equally frightening things—are the main antagonists in The Whispering Skull. In fact, the people involved in Lockwood and Co. must contend with an evil thing called "the Source," which kills anyone that looks inside of it. Compared to the supernatural beings that they go head-to-head with, Lockwood and Co. have very little power. However, because of their skill and ingenuity, they are able to defeat all of the supernatural beings that they come face-to-face with, showing readers how important it is to work hard and be smart when you deal with beings that are seemingly much more powerful than you are.
Death
Death plays an integral role in the events of The Whispering Skull. It is perhaps the most crucial theme in not only The Whispering Skull but the book series. The main investigation in the novel involves a dead man named Edmund Bickerstaff, whose coffin Lockwood and Co. are asked to seal. Initially, things go well for Lockwood and Co. and they can successfully close the coffin. However, they also accidentally release an evil phantom who is bent on destruction. Like Edmund Bickerstaff, that phantom (and nearly all of the supernatural beings that Lockwood and Co. deal with) is a person who has died. Lockwood and Co., in other words, are in the business of dealing with dead people. But they deal with those dead people in a reasonable, respectful, and empathetic way despite many of the supernatural beings wanting to kill them.
