Sherlock Holmes is usually considered the protagonist in any of his stories. Helen Stoner comes to him for help because she fears her life is in danger. The prime suspect is her stepfather Dr. Grimesby Roylott. The author, Sir Arthur Conan Doyle, has Dr. Roylott put in an appearance at 221B Baker Street shortly after Helen leaves. This meeting between Holmes and Roylott is necessary to establish that Dr. Roylott is Holmes' opponent, or the antagonist. The violent and half-mad Roylott establishes the conflict during his short appearance at Holmes' residence.
“I will go when I have said my say. 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.
Dr. Roylott does not appear in the story again until after he has been bitten by his own poisonous snake and is found sitting dead in his room. But his existence as a threat has been established, and it hovers like a black cloud over Stoke Moran. He seems fully capable of killing Holmes and Watson if he found them snooping around inside his house. No doubt he would have a number of guns to choose from on a country estate. When his body is discovered it shows that Holmes has been victorious in their conflict. In the very last paragraph of the story he accepts responsibility for Roylott's death.
"Some of the blows of my cane came home and roused its snakish temper, so that it flew upon the first person it saw. In this way I am no doubt indirectly responsible for Dr. Grimesby Roylott's death, and I cannot say that it is likely to weigh very heavily upon my conscience.”
There is only one protagonist and one antagonist. Dr. Watson accompanies Holmes because he is the narrator and has to observe everything from the first appearance of Helen Stoner at 221B Baker Street. But Holmes is the protagonist and Roylott the antagonist. Helen Stoner might be called "the bone of contention" or "the MacGuffin."