Moscow, 1882. When Fandorin returns from Japan with his manservant Masa, he enters the service of Moscow governor Prince Dolgoruki. Later that day, the White General Mikhail Sobolev, nicknamed the Russian Achilles and an old friend of Fandorin's, is found dead in the same hotel. Officially, he died of a heart attack, but Fandorin becomes suspicious when he talks with the body guards of the general. Fandorin had befriended these cossacks when he rooted out a Turkish spy during the siege of Pleven (see The Turkish Gambit). But the same cossacks now treat him with hostility.
Fandorin finds out the reason for their hostility as he discovers that the general had not really died in the hotel, but was moved there from the apartment of his mistress. Found dead in a compromising situation, the cossacks tried to prevent a scandal and protect the reputation of the general. But Fandorin looks even deeper and finds out that a large sum of money is missing. He learns that Sobolev is trying to raise funds to begin a political campaign, and Fandorin begins to suspect foul play. He finds that the general has been poisoned in a very clever manner, and the killer anticipated the cover up, which would ensure his safe getaway. Fandorin further discovers that the plot leads up to the highest levels of the Tsar's government, and that he himself is now viewed as an enemy of the state for his efforts to catch the killer.
The killer is Achimas Welde, a hired assassin, who has only failed three times in his career. One of those times was his assignment to kill Fandorin, when he just managed to kill Fandorin's wife, as Fandorin himself was chasing him (see The Winter Queen). The second half of the novel is told from Achimas' point of view and recounts his life story, up to the plot to kill Sobolev and the investigation. By chance, Achimas discovers that the man who hired him to kill Sobolev was Grand Duke Kirill Alexandrovich, the younger brother of Tsar Alexander III. In the concluding chapters of the novel, Fandorin kills Achimas, and prepares to flee Moscow (believing himself to be a target of the plotters), but Prince Dolgurukoi's assistant meets him at the train station and tells him that everything has been covered up and he can continue in the service of the state.
The novel features a cameo appearance by Sister Pelagia, heroine of her own series of three Akunin mystery novels, demonstrating that the Fandorin and Pelagia books occur in the same fictional universe.
The governor of Moscow, Prince Dolgoruki, shares his surname with the founder of Moscow, Yuri Dolgoruki. Grand Duke Kirill Alexandrovich, the Tsar's brother, is a fictional character, although he could be modeled after Alexander II's real younger brother, Vladimir Alexandrovich.
As the title of the novel suggests, The Death of Achilles alludes to one of the main characters of the Iliad. However, the allusion is more complex than just the mere reference to general Sobolev's nickname, the Russian Achilles. In fact, the "true" Achilles referred to in the title is the killer, Achimas Welde. The second part of the novel, which recounts the expert assassin's life story, is a cleverly disguised retelling of the Iliad and other Greek myths relating to the life of Achilles. Some clues are scattered within the novel for the informed reader to decipher, such as the following:
The novel's title, therefore, has a double meaning. The real death of Achilles it refers to occurs not at the beginning but in the end of the book. Sobolev's role in the novel, in spite of his nickname, is that of Hector, Achilles' victim. A funeral speech delivered by the Grand Duke midway through the novel, in which he directly compares Sobolev to Hector, offers a more direct clue. This is one of the more complex and broad allusions to famous works of literature which are quite numerous in all Akunin's novels.