When the novel opens, it's 1954. A local fisherman, Kabuo Miyamoto, is on trial for murdering another fisherman, Carl Heine, Jr. The story starts on the very first day of the trial, when the prosecution opens its case. The court hears testimony from sheriff Art Moran, the coroner who examined Heine's body, and Etta Heine (Carl's mother). Through this testimony, the prosecution advances a theory that the murder was premeditated, and that Kabuo Miyamoto wanted to kill Carl over a land dispute between their two families dating back to before World War II. Ishmael Chambers, a local newspaper reporter with close past ties to Miyamoto's wife, Hatsue, is there reporting… and creepily watching Hatsue.
Throughout the story, we jump back and forth between the present day and the characters' memories of life before and during World War II. We learn that Hatsue and Ishmael had a romance that ended when she left for the Japanese internment camp Manzanar in 1942. Soon after that, Ishmael himself went to war, where he lost an arm and generally became a miserable and unpleasant person. We also learn how Hatsue ended up with Kabuo and get various other pieces of background about the characters and their families.
On Day 2 of the trial, Dr. Sterling Whitman, the hematologist who examined blood evidence from the "crime" scene, testifies for the prosecution. The prosecution also calls three fishermen who were out on the water the night Heine died, as well as Sergeant Victor Maples, who trained Kabuo in hand-to-hand combat. Then Carl's wife, Susan, testifies, and we get a lot of flashbacks to her life with Carl. Right after Susan finishes on the stand, the power goes out; apparently a snowstorm storm put the power out all over the island.
In light of the outage (pardon the pun), the trial judge decides to adjourn until the next day. After stocking up on some supplies and getting his car ready to travel, Ishmael heads out to visit the local coast guard office (to do research for a story about the storm) and to make sure his mother is okay. On his way, he runs into Hatsue and her father, who have had a car accident. He gives them a ride back to their house, at which point Hatsue tells him to write a story about how unfair the trial has been. Ishmael basically blows her off by saying that life is just kind of unfair and we all need to deal with it (in other words, tough noogies). After dropping them off, he continues on with his plans.
At the coast guard office, Ishmael suddenly realizes he might find some information relevant to the trial there. After about 15 minutes, he finds evidence that Carl likely fell off his boat when a freighter passed near to where he was fishing, which would have created major waves. To document his discovery, Ishmael sneaks out three pages from the records. Then, he heads to his mother's, where he ends up spending the night.
However, Ishmael's actions from there are not what you would probably expect. Instead of resolving to bring the evidence he found to the court, Ishmael decides he's actually going to sit on it and instead write the story that Hatsue suggested about the trial's unfairness. Why? Apparently he thinks it will curry favor with her so that, after the trial, she'll remember he sided with her. It seems that he has the idea that Hatsue might come sniffing around again if her husband isn't set free. Charming boy, no?
The next day, Kabuo and Hatsue both take the stand and offer their accounts of what happened the day Carl Heine died. The trial wraps up with closing arguments and reminders to the jury about their duties in weighing the evidence and arriving at a verdict. When they start deliberating, it's clear that all of the jurors want to convict except one.
Later that evening, Ishmael is at his mother's, continuing to sort through old memories. He decides to let Hatsue go finally. He heads over to her house and delivers the evidence he found at the lighthouse.
The next day, Hatsue shows up at his house early. She wants to check Carl Heine's boat for a lantern rigged up to the mast, which would corroborate Kabuo's story and help exonerate him completely. Hauling tail to town before the jury reconvenes at 8 a.m., they go and show Art the shipping records that create an alternate explanation for Heine going overboard, which helps convince him to go take another look on the boat for the evidence Hatsue and Ishmael think might be there.
They don't find the lantern, but they do come across evidence that it had been there. Also, they find proof that Carl's hand was cut (as Kabuo had testified) and that he had actually gotten his head wound by hitting his head on the boat when he fell over—and, as the prosecution claimed, through Kabuo's semi-mythical kendo skills. As a result of these findings and the evidence Ishmael had found, Kabuo is exonerated.