Summary
Watson, Holmes, and Jones have a lively meal together, before getting back to figuring out the crime as they pass several bridges by boat to reach Jacobson's Yard. There they finally find the Aurora. They realize that she is a very fast boat and they will have trouble catching up to her. They race after her until they get close enough to see the people on the deck, spying one very small black man, with a mean face.
The man starts to pull out a small piece of wood and puts it to his lips, but before he can do anything else, both Watson and Jones shoot at him. The man coughs and chokes before falling overboard into the river. The captain of the boat, Mr. Smith, and his son sit on the deck and come aboard Holmes' ship when told to.
The group finds a solid iron chest full of treasure on the Aurora–the treasure that was stolen from Sholto. Upon closer examination, Holmes finds out that the small man did have time to fire when Watson and Jones fired upon him, except he fired a poisonous dart from a pipe at his lips, which just narrowly missed Watson and Jones.
The group looks for the small man in the water, but can't find any trace of him in the Thames. Holmes and Watson speak with the captain, Mr. Jonathan Small. He reveals that it was the small man, Tonga, who killed Sholto, and that he (i.e. Small) had no part in it. They make sure that Mr. Smith had no part in this, and was simply an innocent bystander who got roped into helping Tonga.
Watson goes with the iron chest to Miss Morstan. Though happy to give Miss Morstan back her half of the treasure, Watson is sad that the case is over and that he won't get to spend more time with her. He recounts how they found the chest at her request.
They go to open the Agra treasure chest, only to find that it is completely empty! Watson expresses relief, because now Miss Morstan is within his reach again, romantically speaking: she is no longer impossibly rich. He confesses his love to her, and she, too, expresses relief.
They tell Mr. Small the news about the empty chest and he laughs, saying that he has put the treasure away and no one will ever lay a hand on it. He confesses that he threw the treasure in the river, but Jones doesn't believe him. Small is angry and decides to tell his side of the story.
He details his time as a soldier in India and how much bad luck he endured, until it all seemed to change when he met Abel White, who got him a good job. Then a mutiny occurred and the rebels set fire to White's home. Small went on watch as a guard against the rebels and was surprised one night by a man with a knife, who offered him the chance to become rich.
The man revealed a plan to steal the treasure of a wealthy rajah who entrusted it to a traveling merchant, Achmet, who was currently in the city of Agra. The merchant approached the gate and spoke with Small, asking for passage, unaware that the guard, Small, was in cahoots with robbers. They killed the man and took the treasure, which was full of precious gems. The officials found the body and sent Small to a different settlement where he soon enough met Sholto, Morstan, and Brown at a card game.
Small told Sholto, Morstan, and Brown about the treasure and asked that they free him in exchange for a fifth of the treasure each. They made a plan with three other accomplices; Sholto was to go to India and hide the treasure. However, as we know, he wasn't heard from again, spurring Small to hunt him down. Small partnered with Tonga after nursing him back to health.
They found Sholto and kept tabs on the happenings at Pondicherry Lodge for years, realizing that they were also looking for the treasure. Small learned about he trapdoor and took the treasure, surprised that Tonga had killed Sholto, which had not been part of the plan. So although Small was betrayed by Major Sholto, he had nothing to do with the death of Sholto's son, Thaddeus Sholto.
Having solved the case, Watson reveals that he and Miss Morstan are to be married. Holmes groans at the emotional aspect of this, but he congratulates Watson all the same. The story ends on an ominous note as Holmes reaches for his cocaine bottle as the constant companion in his life. Watson muses that Holmes did all the work but got none of the reward.
Analysis
Here we realize that throughout the story, in small ways and paragraphs, Watson has slowly been falling in love with Miss Morstan, and that she, likewise, has an affection for the doctor–an affection we see, for instance, when she blushes upon his surprise arrival at her home.
The treasure of Agra made Mary impossible for John to attain, since she would have probably preferred a richer or posher man to a normal doctor. But once the treasure is gone, Watson is incredibly relieved for he realizes that he can keep the treasure that is Mary, instead of losing her to someone else.
Holmes also reveals that Jones was actually right in one sense: in order to accomplish their scheme, Tonga and Small had to have an accomplice within the house to aid them. In this case, it was really was the butler who helped them, Mr. Lal Rao.
Watson got a wife, Jones gets the glory, but Holmes is happy with his cocaine. This foreshadows future problems and continued loneliness for Holmes, who it seems will remain a confirmed bachelor throughout his adventures.
