The first clues that help Holmes solve the mystery are derived from his investigation into the estate of Helen and Julia's mother. From this, Holmes determines that if either Helen or Julia marries, Dr. Roylott's finances would be severely impeded; if both were to marry, he would be in financial ruin. This clearly gives Dr. Roylott a motive for the murder(s).
Next is Dr. Roylott's demand that Helen move into a particular room in his home, Stoke Moran. This seems a strange request and leads Holmes to believe that this room must, in some way, present Dr. Roylott with the opportunity to carry out his crime. Now, motive and opportunity have been established, Homes and Watson only have to infiltrate the room and await for the details to reveal themselves.
From the seemingly pointless ventilation shaft and the equally useless bell rope, Holmes is able to deduce that these two elements must be involved in the murder attempt in some way--why else would they be there? From the other details of of the whistling sound, the metallic clank, and the exotic pets that Dr. Roylott keeps on the grounds, Holmes deduces that some sort of animal must make its way through the vent and down the rope toward its victim.
Holmes only has to await the arrival of the swamp adder to confirm his theory.
There are at least three things that Sherlock Holmes would notice that would make him think that Roylott is the one who has killed Julia and is trying to kill Helen. These are all things that Roylott has done that do not make a lot of sense if he is not the murderer.
- Why does he have Helen move into the room where Julia died?
- Why did he have this vent constructed that does not lead to the outside? It just goes to another room -- that makes no sense.
- Why does he put in this bell pull that is not attached to a bell?
All of this stuff makes no sense so it must be connected to the murder.
There are other suggestive circumstances that should make the reader suspect that Dr. Roylott is responsible for the death of Julia Stoner and is trying to murder her sister Helen. These are not exactly clues but details of great significance. One is that Grimesby is a doctor. This, of course, suggests that he should know a great deal about poisons and could know of a type of poison which is undetectable in an autopsy. If such an undetectable poison existed, Roylott was the kind of man who would have found out about it.
Another striking detail has to do with money. Roylott would have been legally obliged to pay Julia a large sum of money if she got married and would have been obliged to do the same to Helen, who was engaged to be married within as little as one month.
She [the mother] had a considerable sum of money—not less than £1000 a year—and this she bequeathed to Dr. Roylott entirely while we resided with him, with a provision that a certain annual sum should be allowed to each of us in the event of our marriage.
Roylott is hard up for money and has his estate mortgaged for more than it is worth. He would face financial ruin if he had to pay either of his stepdaughters the money they are entitled to.
Roylott has spent many years in India and seems to know a lot about exotic Indian animals. The cheetah and the baboon symbolize his esoteric interests.
Roylott associates with a band of rather mysterious gypsies, who could conceivably aid and abet him in killing his stepdaughters. These gypsies might know of undetectable poisons.
Dr. Roylott shows that he has a terrible temper. He served a long term in prison in India for killing a servant. He is hated and feared by everybody in the neighborhood of Stoke Moran. When he bursts into Holmes' room at Baker Street he makes a display of his strength, temper, and potential violence.
“Don't you dare to meddle with my affairs. I know that Miss Stoner has been here. I traced her! I am a dangerous man to fall foul of! See here.” He stepped swiftly forward, seized the poker, and bent it into a curve with his huge brown hands.
“See that you keep yourself out of my grip,” he snarled, and hurling the twisted poker into the fireplace he strode out of the room.
The reader is sure that Dr. Roylott is responsible for Julia Stoner's death and is trying to murder her sister Helen. Roylott is a "prime suspect." The only question is how he could manage to do it.