The novel consists of two distinct sections:
- Part 1: Set in 1905, with Fandorin now 49 years old. As the Russo-Japanese War breaks out, Fandorin temporarily returns to Russian state service, albeit as a railroad engineer, rather than an investigator. However, when a crafty Japanese spy operating under the alias "Captain Rybnikov" starts derailing Russian trains, Fandorin's detective skills are once again called for.
- Part 2: Jumping back to 1878, Fandorin serves as a diplomat in the Russian consulate in Yokohama, but is soon drawn into an investigation of a series of political murders rumored to have been perpetrated by the ninjas. This section fills in the part of Fandorin's life that was previously a Noodle Incident between Fandorin books #3 and #4, detailing how Fandorin trained in the ways of the ninja while in Japan, and how Masa entered into Fandorin's service as a valet and Heterosexual Life Partner. Part 2 is over three times longer than Part 1.
This book introduced Anachronic Order to the Fandorin series as a whole. While the first 9 1/2 books followed Fandorin's career chronologically from 1876 to 1905, later novels would increasingly use flashbacks. The next Fandorin novel translated into English was Fandorin #12, All the World's a Stage. Fandorin #11, short story collection Jade Rosary Beads, was skipped.
- Author Appeal: Boris Akunin the Japanophile and professional Russian-Japanese translator really cranks it Up to Eleven in this installment. Lots and lots and lots of talk about Buddhism and the way of the ninja. Near the end the plot basically halts for a whole chapter while Fandorin and Masa study at a ninja training camp.
- The spy reads from a newspaper listing the fallen at Tsushima, including Commodore Endlung and State Counselor Ziukin. Those are characters from The Coronation, with Ziukin being the narrator of that book; at one point in The Coronation naval officer Endlung suggests that Ziukin should join the navy as well.
- After Fandorin arrives in Yokohama, Doronin says that he was supposed to arrive a week earlier; Fandorin blushes and says he overslept and missed the boat leaving Calcutta. The real reason is that Clarissa Stamp held Fandorin back in Calcutta after the events of Murder on the Leviathan, for a week of sex.
"Russia was seriously ill, running a high fever....The empire had become an anachronism, a dinosaur with a body that was huge and a head that was too small, a creature that had outlived its time on earth....hidden at the center of this head was a tiny little brain, uncomplicated by any convolutions....deep in the entrails of the new behemoth, a deadly tumor was burgeoning.
- "....There are already too many empires in the world—any minute now they will all start wrangling with each other." Doronin, Fandorin's boss at the Russian consulate in Yokohama. He also foresees the collapse of those empires, as well as Japan's expansion into continental Asia and confrontation with Russia.
- In Part I, Fandorin is desperately worried about the state of Russia.
- Towards the end of Part I Fandorin despairs about Russia again, thinking that if violent rebellion breaks out it's all over, that even if the government crushes the revolution this time, it will fall in a few years "during the next convulsion". Which of course is what happens: violent rebellion breaks out in 1905 and is crushed, but the stage is set for the revolutions of 1917.
- A Death in the Limelight: Fandorin is the POV character for most of the second part, but three of his fellow investigators get their own POV chapters, in order, where each of them is killed off.
- Delivery Not Desired: At the end of part 1, the captured spy writes a letter to his long-lost-but-recently-found father, then burns it and commits suicide.
- Duel to the Death: Fandorin fights one with Bullcox.
- Femme Fatale: O-Yumi-san aka Midori, a high-class courtesan and a ninja.
- Heroic BSoD: Fandorin after the faked death of his beloved Midori-san.
- Historical In-Joke: How does the Russian Revolution of 1905 blow up? Due to weapons smuggled to the revolutionaries by a Japanese spy.
- It Will Never Catch On: In the second (1878) part, Fandorin regards the notion that Japan could transform itself into a great power in thirty years as "simply laughable".
- Learned From the News: Fandorin reads a newspaper article about the Battle of Tsushima, only to discover the names of his two compatriots from The Coronation on the list of officer casualties.
- Luke, You Are My Father: Though Fandorin himself never knew that "Rybnikov" was his son by Midori.
- Ninja: Fandorin and the Tamba Clan in Diamond Chariot, including his own son.
- Old Master: Momochi Tamba, the head ninja.
- Please Kill Me If It Satisfies You: The head of a ninja clan offers Fandorin a chance to kill him to take revenge for his friends whom the ninjas slaughtered earlier. He doesn't technically have to atone for this, of course (since he is a ninja, after all), but he needs Fandorin's trust.
- Reed Snorkel: "Rybnikov" tries to escape via the river using one of these, but Fandorin sees it and pinches the snorkel shut.
- Spy Drama: Part I has Fandorin hunting a Japanese spy sabotaging the Trans-Siberian Railway. Part II explains the origins of that spy.
- Switching P.O.V.: In the first (1905) part the POV switches back and forth between Fandorin and the Japanese spy he's chasing. Also happens in the second (1878) part, see A Death in the Limelight above.
- Tear Off Your Face: Twice.
- Villain Opening Scene: The first scene features the Japanese spy receiving a secret parcel and then murdering the Okhrana agent tailing him.
- Whole Episode Flashback: In fact, the last 3/4 of the book is an extended flashback.
- Yakuza: The Diamond Chariot. Masa is a former criminal, whose life and honor Fandorin accidentally saved.