On the evening of November 26, 1941, Detective Joe McGrady of the Honolulu Police Department is called back to headquarters by his supervisor, Captain Beamer, and briefed on a body found at a remote dairy farm in Kaaawa Valley on Oahu's windward side. McGrady, a former Army captain who served with Marines in China before settling in Hawaii, drives over the mountains to the equipment shed and finds a young white male hanging upside down from a meat hook, disemboweled. When he returns after calling for backup, a scar-faced man stands by a stolen Packard coupe with a bucksaw and gas can, preparing to destroy the evidence. The man opens fire. McGrady kills him with his Army-issue .45 and finds blood and a long black hair in the Packard's trunk. With backup, he searches the shed further and discovers a second victim: a young woman, naked and bound, beaten with a Mark I trench knife, a World War I-era weapon combining a dagger blade with spiked brass knuckles. Her throat has been slit. McGrady concludes the scar-faced man had a partner.
Autopsies at Tripler Army Hospital yield a critical identification. Colonel Underhill, the Army surgeon, recognizes the young man and summons Admiral Kimmel, commander of the Pacific Fleet, who confirms the victim is his nephew, Henry Kimmel Willard, a twenty-one-year-old student of Japanese being groomed for Naval Intelligence. The scar-faced man's autopsy reveals an old American bullet in his hip and scars suggesting he is a German veteran of the Great War. Paired with Detective Fred Ball, McGrady searches Henry's bungalow and discovers someone removed all his study materials after Kimmel's staff checked the house. A black hair in the drain and perfume on the pillows suggest Henry had a female companion, and an unmatched thumbprint from Henry's abandoned car confirms a second killer.
The case escalates when businessman John Kincaid of Alexander & Baldwin convenes a meeting with the governor, FBI, and military leadership. Kimmel reveals that a Marine named Vincent Russo was found murdered with identical wounds on Wake Island. FBI agent Bob Shivers reports that a man booked as "John Smith" bought a one-way Pan Am Clipper ticket to Hong Kong the morning after the murders, using a fraudulent passport. McGrady is sent to fly the Clipper route. Before departing, he deepens his bond with his girlfriend, Molly, a twenty-nine-year-old graduate student at the University of Hawaii.
Following Smith's trail westward, McGrady arrives in Hong Kong on December 7, 1941. He meets Emily Kam, a half-Chinese young woman who encountered Smith during the Clipper journey and agrees to draw his portrait from memory. By evening, McGrady has traced Smith to the Empire Hotel in Sheung Wan. Before he can act, Hong Kong police arrest him on a fabricated rape charge; McGrady realizes Smith orchestrated the frame-up. Nathan De Vries, a young American consulate official, visits McGrady's cell but is too frightened to intervene. On December 8, the Japanese attack across the Pacific. McGrady is abandoned in his cell as Hong Kong falls. Japanese soldiers bayonet prisoners in the cell block but spare McGrady when he identifies himself as American. On a ferry dock, Emily finds him behind the wire and tells him Japanese soldiers murdered her father, with Smith present, speaking Japanese. McGrady gives her his remaining money and urges her to survive.
McGrady is shipped to Yokohama. Upon arrival, he is brought before Takahashi Kansei, first deputy to Foreign Minister Togo Shigenori, who identified McGrady from the
Honolulu Advertiser. Takahashi reveals the murdered woman was his niece, Takahashi Miyako, a translator from Admiral Yamamoto's secretarial pool who transferred to the Japanese consulate in Honolulu. He offers to hide McGrady in his Tokyo home for the war's duration in exchange for a promise to find Smith afterward. At Takahashi's house in the Yanaka neighborhood, his daughter Sachi, a twenty-five-year-old former Foreign Ministry clerk fluent in four languages, privately tells McGrady what her father does not know: Miyako learned the details of the Pearl Harbor attack and sought the Honolulu posting to warn the Americans. Takahashi has paid the camp commandant to falsify records showing McGrady was executed, meaning everyone, including Molly, believes he is dead.
Over more than three years, Sachi teaches McGrady Japanese in daily lessons that gradually deepen into love. He writes nightly letters to Molly for over a thousand days, then burns them when he realizes she believes him dead. On March 9, 1945, McGrady and Sachi confess their feelings and become intimate. That night, American B-29s firebomb Tokyo. A young Kenpeitai (military secret police) soldier enters the house to enforce the blackout, finds McGrady in Sachi's bed, and reaches for his weapon. McGrady breaks the boy's neck. Sachi, who recognizes the soldier as a neighborhood boy she once babysat, is devastated. She departs for the family's mountain home in Nozawaonsen, leaving a note that she loves McGrady but cannot remain.
Japan surrenders on August 15, 1945. McGrady returns to Honolulu, where Fred Ball tells him he married Molly in January 1944. They have a one-year-old son named Joe. When Molly later asks if McGrady would take her back, he tells her no: She has a husband and a son.
Reinstated at HPD and soon fired after beating Ball in the station basement for brutalizing a suspect, McGrady works alone with Emily Kam's drawing of Smith. Through Chinatown contacts, he traces leads to a house at 1547 Liholiho Street, which proves to be a safe house filled with propaganda from the German-American Bund, a pro-Nazi organization that operated in the United States. Through the kitchen window, McGrady sees the homeowner: Captain Beamer. He realizes Beamer facilitated Smith's operations and sabotaged the investigation. McGrady persuades Ball to help by invoking their old partnership and promising the biggest case of Ball's career. They interrogate Beamer, but he grabs a hidden revolver when their backs are turned, and McGrady shoots him dead. Beamer dies without revealing Smith's real name. In a cable company's archives, McGrady finds Beamer's 1941 warning addressed to "John Smith, c/o Golden Phoenix Transshipping, Sheung Wan," Hong Kong.
McGrady arranges military transport and returns to Hong Kong in late December 1945, tracing the Golden Phoenix to an active cable account. He intercepts an encrypted message in Wabun, a Japanese telegraphic code Sachi taught him, revealing Smith is forging documents for fleeing war criminals. At the U.S. consulate, De Vries, now Acting Consul General after wartime service in France, introduces McGrady to a local-hire employee called "Jan Van Dijk." McGrady recognizes the face from Emily's drawing: Van Dijk is John Smith. Smith discovers McGrady's identity and lures him to a cottage on the Peak, where he reveals he was an Abwehr (German military intelligence) officer and attempts to negotiate. When McGrady refuses, Smith draws a pistol, but De Vries bursts through the door and takes a bullet in the shoulder, giving McGrady his opening. McGrady drives a trench knife he had brought with him into Smith, whispering that Takahashi Kansei and Admiral Kimmel sent him.
On Christmas night, McGrady climbs the Peak to tell Emily Kam that Smith is dead. He then flies to Tokyo and takes a train north, setting out on foot through deep snow for the final 15 kilometers to Nozawaonsen, losing his suitcase and nearly freezing. Sachi opens the door, leads him around the house to a natural hot spring pool, and guides him into the water, holding him as his body thaws. As he recovers in her arms, McGrady taps a message against the skin of her wrist in Wabun code, the language of touch she taught him, communicating what he has carried across the Pacific and through five Decembers.