The story is set in 1888. The Sign of the Four has a complex plot involving service in India, the Indian Rebellion of 1857, a stolen treasure, and a secret pact among four convicts ("the Four" of the title) and two corrupt prison guards. It presents the detective's drug habit and humanizes him in a way that had not been done in the preceding novel, A Study in Scarlet (1887). It also introduces Doctor Watson's future wife, Mary Morstan.

According to Mary, in December 1878, her father had telegraphed her upon his safe return from India and requested her to meet him at the Langham Hotel in London. When Mary arrived at the hotel, she was told her father had gone out the previous night and not returned. Despite all efforts, no trace has ever been found of him. Mary contacted her father's only friend who was in the same regiment and had since retired to England, one Major John Sholto, but he denied knowing her father had returned. The second puzzle is that she has received six pearls in the mail from an anonymous benefactor, one per year since 1882 after answering an anonymous newspaper query inquiring for her. With the last pearl she received a letter remarking that she has been wronged and asking for a meeting. Holmes takes the case and soon discovers that Major Sholto had died in 1882 and that within a short span of time Mary began to receive the pearls, implying a connection. The only clue Mary can give Holmes is a map of a fortress found in her father's desk with the names of Jonathan Small, Mahomet Singh, Abdullah Khan and Dost Akbar.

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