What does Holmes learn when he starts to question Mr. Wilson about his assistant?

During the interview, Holmes learns that the assistant's name is Vincent Spaulding. That he is around thirty years old. That he has a avid interest in photography and is always diving down into Wilson's cellar to develop his pictures. That he came to work for half-wages to learn the business. That it was he who called Wilson's attention to the ad for red-headed applicants to the fictitious league.

Towards the end of their interview, Holmes brings up his most important questions.

“What is he like, this Vincent Spaulding?”

“Small, stout-built, very quick in his ways, no hair on his face, though he's not short of thirty. Has a white splash of acid upon his forehead.”

Holmes sat up in his chair in considerable excitement. “I thought as much,” said he. “Have you ever observed that his ears are pierced for ear-rings?”

“Yes, sir. He told me that a gipsy had done it for him when he was a lad.”

Holmes already feels sure that Vincent Spaulding is really a notorious criminal named John Clay. The detective is excited because he has been trying to capture Clay for a long time, and he knows that Scotland Yard would also like to get their hands on him. Holmes feels sure that Clay is working for Wilson for an ulterior objective and is probably going down to the cellar because he is digging a tunnel.

Watson describes Wilson as a "stout, florid-faced, elderly gentleman." This is to forestall any reader's question as to why Wilson never goes down into his own cellar to see what his assistant is doing. The "florid face" suggests high blood pressure. He would not want to venture down a steep flight of wooden stairs and climb back up again just out of curiosity. If he had ever done so, he would have ended up buried in his own cellar, because Clay would have no compunctions about murdering him.

When Holmes and Watson inspect the vicinity of Wilson's pawnshop, Holmes deduces that the tunnel is being dug in the direction of the Coburg branch of the City and Suburban Bank. Since the Red-Headed League had been dissolved that very day, Holmes further deduces that the thieves are planning to break into the bank's basement strong room and loot all its stored gold via their tunnel that very night. He sets up a trap and both are caught. Clay will hang for this and previous crimes.