Alice believes that James is innocent and has contacted Inspector Lestrade, who in turn seeks help from Sherlock Holmes.
She also believes that she was the subject of the argument between the McCarthys – Charles wanted his son to marry her, but James had refused.
Holmes asks Alice if he could meet her father, but she says his health worsened after the death of Charles, whom he had known since they were in Victoria.
What she does not know is that James actually loves her but could not follow his father's demand because he had married a barmaid before Alice had returned from boarding school.
After examining the ground, Holmes finds evidence of the presence of another man, besides Charles and James, whom he believes to be the murderer.
At the hotel, Holmes explains to Watson that "Cooee" is an Australian cry and that the apparent reference to "a rat", overheard by James, in fact comprised the last syllables of "Ballarat", a place in Australia.
John Turner, Alice's father, then comes to their room (coincidentally being announced by a hotel employee right as Watson is about to name him as the killer, after correctly interpreting the hints Holmes has offered him), entering with a limp, and, realising that Holmes has deduced the crime, confesses.
Although he liked James, John did not want Charles' "cursed blood" mixed with his family's, so he resisted the union.
However, he became angry when he heard the nature of the argument and killed Charles to preserve his freedom and spare his daughter.
Meanwhile, Watson surmises that James and Alice will likely marry and live in happiness without ever discovering the true history of their fathers.
En route to the murder scene Holmes tells Watson that "Boscombe Valley is a country district not very far from Ross, in Herefordshire."
Leslie S. Klinger, in his The New Annotated Sherlock Holmes, calls it "a disguised name" and lists possible locations for the setting of the story as posited by other researchers.
[8] Lestrade is replaced by a local policeman, Inspector Lanner, and Charles McCarthy's first name has been changed to Bill.
In the 1991 TV adaption starring Jeremy Brett and Edward Hardwicke, Boscombe Valley is in Cheshire in the northwest of England.
[11] In 1943, the BBC Home Service dramatised the story with Arthur Wontner as Holmes and Carleton Hobbs as Watson.
The episode, which featured Kevin McCarthy as Sherlock Holmes and Court Benson as Dr. Watson, first aired in May 1977.