It is the winter of 1954, about ten years after World War II. On San Piedro Island, a fictional island set in Puget Sound in Washington, a Japanese-American born in the United States is facing the charge of first-degree murder. Kabuo Miyamoto is on trial for the death of Carl Heine, a fellow fisherman and his old childhood friend. The narrative begins with the trial, as the prosecution sets forth its case. As the trial progresses, the history of the island community and the individual characters are revealed as a tightly knit web of relations.
Carl Heine's boat was spotted floating on its side, and when the sheriff and his deputy investigated the boat, they found Carl Heine drowned and tangled in his fish net. An odd wound on the left side of his head triggered an investigation. The coroner, upon examining the wound, stated that it reminded him of the wounds made in close combat with the Japanese during the war, often made by kendo techniques. The coroner also concluded that the cause of death was drowning, because Carl had hit the water breathing, which the presence of red foam indicated. Additional evidence points in the direction of Kabuo and Carl having had an encounter that night on the sea: the mixture of engines between their boats, a mooring line on Carl's boat that resembled all of Kabuo's, and the presence of Carl's blood on the handle side of a rope with a fishing gaff, which the prosecution hints was the murder weapon. Each piece of evidence is challenged by the defense attorney, Nels, to shed doubt on the prosecution's case.
During the recess, Ishmael Chambers, the head of the San Piedro Review, which he had inherited from his father Arthur, watches Kabuo and his wife Hatsue speak to each other. In a flashback, it is revealed that Ishmael and Hatsue had been children together and that, at the age of ten, Ishmael had taught her to swim. At sea, they had shared their first kiss, and as they grew older they became young sweethearts, meeting in secret. When the Japanese people in the community had been relocated by executive order to the Manzanar camp in California, their love affair ended: Hatsue's mother had discovered it, seeing a letter Ishmael had written to Hatsue. In the end, though, Hatsue and Kabuo had grown closer at the camp, and they married shortly before Kabuo went to fight in the war in the European theater.
The issue then turns to Kabuo's family, the Miyamotos, and the witness Etta Heine. Etta is the mother of the deceased, and she presents the story of how her husband, Carl Senior, had entered into an amicable but quasi-legal agreement with Kabuo's father Zenhichi for seven acres of their land. It was arranged so that the payments would be finished when Kabuo turned twenty, and Kabuo then would gain title to the land. However, with the relocation, Kabuo's family missed the last two payments, according to Etta. Carl Senior died of a heart attack, and Etta sold all of the land to Ole Jergensen, returning all of the equity back to the Miyamotos. (The value of the seven acres had increased significantly since the time of the agreement.)
Ole Jergensen explains how Kabuo came to him after the war. He had known nothing of the prior agreement with the Miyamotos. After Ole had a stroke, he decided to sell, Carl offered to buy, and they made a deal. Kabuo arrived later that same day, but he was too late. Susan Marie Heine, Carl's widow, testifies on the stand that Kabuo arrived to talk to Carl. They talked for a while outside, and when Carl came in, he told his wife that Kabuo had wanted to buy the seven acres from him--that it was the same old business. He had expressed doubt about the transaction, given the dirty looks his mother claimed Kabuo was always throwing, as well as the fact that he was Japanese. He gave no conclusive answer.
Ishmael then goes to the lighthouse to do some investigating on his own. He examines the lighthouse records and finds that on the night of Carl's death, just minutes before his watch stopped in the water, a large freighter came through the channel with a wake large enough to cause a serious mishap. Ishmael decides not do anything with the evidence just yet. Still thinking of Hatsue, he watches her go to the stand to testify for her husband. He was hopeful, she says, when he came back from talking to Carl. Then, on the morning of September 16, he came back from fishing and said that he had helped Carl with a dead battery at sea, and they had come to an agreement about the seven acres. After Kabuo went to sleep, Hatsue heard the news at one in the afternoon that Carl had been found drowned.
Then the honor code at sea is discussed: fishermen help one another in times of emergency, regardless of personal feelings, because they know that one day they may need the help themselves. In this context the prosecution presents the theory that Kabuo faked trouble with his own engine to lure Carl to bind their boats together, whereupon Kabuo killed him with the fishing gaff. When Kabuo takes the stand and testifies regarding this matter, the evidence seems strong against him: the agreement; the healing of old, deep wounds in the blindness of the fog; Kabuo's expressionless face, which the prosecution suggests is concealing the truth. The judge admonishes the prosecutor for this unfair innuendo, but it is enough for the seeds of prejudice to grow among the jury.
After the closing arguments, the judge gives instructions about following the standards of the law, and then the jury deliberates. One man is unable to see Kabuo as guilty beyond a reasonable doubt, though the rest are ready to convict him. That night, Ishmael decides what to do with the lighthouse notes. He goes to Hatsue, explains the facts, and then in the morning they go together to see the sheriff and his deputy about having another look at Carl's boat. They find traces of what must have been a lantern lashed to the mast in Carl's state of emergency, and then evidence of blood and hair at the top of the mast. By ten in the morning, the jury is dismissed in light of the new evidence, and Kabuo is a free man.
Ishmael photographs Kabuo with Hatsue and then sits to begin writing what the reader can assume will be the facts, the truth, of what happened to Carl that night on the sea. It had been an accident. Within the human heart, one can find a space that can be free of such troubles.