Holmes gleefully examines the crime scene. He observes two distinctive marks on the floor: a footprint and a circular print of a wooden stump. He and Watson agree that the wooden-legged man must have had help; the outer walls of the house are too high for him to have scaled. Someone else must have got inside and lowered him the rope to climb up, hypothesizes Holmes.
Holmes gets a thrill from case work, particularly when he’s actually on the scene of the crime. The wooden stump footprint ties in with Major Sholto’s deathbed story, in which the two brothers found only one footprint in the flowerbed outside of the Major’s window.
Watson wonders how the wooden-legged man’s ally could have got into the room. Holmes is mildly annoyed by Watson, saying, “how often have I said to you that when you have eliminated the impossible whatever remains, HOWEVER IMPROBABLE, must be the truth?” Watson realizes that the accomplice must have come through the hole in the roof.
Holmes and Watson investigate the roof cavity and find a trapdoor leading out on to the roof. Here, they notice another set of footprints—but these are much smaller than those from an average man. Watson thinks a child must have been involved; Holmes clearly disagrees but doesn’t yet explain why. Holmes is satisfied he has gleaned everything there is to learn from the scene.
The second set of footprints sets the stage for Tonga’s entry later in the novella. The disagreement between Watson and Holmes serves to further distinguish their two different intellects.
Holmes notices that the wooden-legged man appears to have stepped in creosote. They hear the police arrive and quickly examine the body. Bartholomew’s muscles are in a state of extreme contraction, suggesting poisoning by “some strychnine-like substance.” Holmes explains that the poison must have been administered by the thorn.
As is often the case in Sherlock Holmes stories, there are convenient and improbable details. Here, the culprit has stepped in pungent creosote and thereby created an opportunity for Holmes to track him. The thorn is confirmed as a foreign object, intensifying the sense of strange outside influence.
Just then, the bumbling and red-faced Scotland Yard detective, Athelney Jones, arrives on the scene. He addresses Holmes patronizingly, calling him “the theorist.” Jones has already made up his mind that Thaddeus is guilty of Bartholomew’s murder. Despite Holmes’ attempt to get Jones to see the holes in his theory, Jones arrests Thaddeus right then and there.
The official police act, and Jones in particular, as Holmes’ foil, creating a low standard against which Holmes’ immense powers can be contrasted.
Holmes tells Thaddeus he will be freed soon enough. He also names the real suspect, Jonathan Small; he adds that he is aware of an accomplice, though does not know his identity yet. Holmes takes Watson aside and asks him to escort Miss Morstan home, before fetching Toby the hound from an associate of Holmes’ to help them track the wooden-legged man.
Holmes’ perception of the case is completely different from Jones’ or Watson’s, once again elevating his powers of deduction as superhuman and uncommon. Toby is going to be used to follow the conveniently pungent creosote scent.