The novel begins with the birth of the protagonist, Thomas Just. He is born in the Native American reservation Dark River, a fictional reservation on the coast of the Pacific Northwest. On the day he is born, his mother holds him up to a giant octopus that is able to walk on land, as a blessing. The novel also recounts the life of Witka, Thomas's grandfather. Witka is described as a mystical man who was able to hold his breath for an incredibly long time and was the whale hunter of the tribe.
Thomas grows up and shares a number of his grandfather's gifts. He marries his childhood sweetheart, Ruth. They are happy together, but then Thomas drunkenly enlists to fight in Vietnam. Ruth is devastated, as she has just learned that she is pregnant. Thomas leaves for war and she raises their son, Marco, alone. Thomas eventually returns to America, but is profoundly damaged by his trauma from the war.
Years later, the tribe plans a whale hunt, but Ruth sees it as a cheap and disrespectful attempt to make money. She sees that is not being killed for food or tribal ritual. At the same time, Thomas returns to the tribe in the hope of finding himself again. He comes back to the reservation but ignores Ruth and refuses to meet Marco. Marco becomes involved in the hunt as well and is selected to listen for the whale. They successfully kill the whale, but Marco's canoe capsizes. The men treat the whale's body disrespectfully, upsetting Thomas, who thinks they have forgotten the tribe's values. Marco does not return and is not found. A man claims to have seen Marco get pushed and held under the water by a man with a ring, but no one takes his suggestion seriously.
Thomas deteriorates rapidly, moving into Witka's old home and becoming a recluse. Life on the reservation becomes difficult after the whale hunt. There is a period of drought and the ocean recedes. Ruth asks a man known as the Rain Priest for help. He tells her she must sacrifice her boat as an offering. It rains for several days after this. Thomas decides to go to Washington D.C. to return the medals he was awarded. It is revealed that he left behind a daughter named Lin in Vietnam.
The novel then flashes back to Thomas's time in Vietnam. He does not fit in in his platoon because he does not desecrate the bodies of dead Vietnamese combatants and civilians, like the other soldiers. At one point, they attack a village of only women and children. Horrified by the other men, and seeing no other option, Thomas kills them to prevent them from massacring the village. He does not come home initially, and is reported missing, because he fakes his death. He leaves his dog tags in a ditch to suggest that he has been captured or killed. He marries a Vietnamese woman and they have a daughter, Lin, together. The woman is killed by a landmine and Thomas is found by American authorities at her funeral and taken back to the U.S. He is haunted by the image of Lin running toward his helicopter.
The novel switches to Lin's perspective. She grows up as an orphan after her mother dies and her father is taken back to the U.S. She narrowly survives multiple encounters with the Vietnamese military. She is homeless for a time in Ho Chi Minh City but is eventually taken in by a florist and his wife. Initially, the florist's wife doesn't like her, but eventually grows close to her. Lin excels in school and also meets her future husband. Coincidentally, her husband ends up being a soldier who saved her many years before. Lin decides, after years pass, to travel to America and meet her father, as a grown woman.
Lin flies to Dark River and meets Ruth, who she grows to like very quickly, recognizing her strength and direct honesty. Ruth takes Lin to meet Thomas, who is unable to express himself or his feelings to her. Lin brings a red fish with her, hoping to remind Thomas of the fish he gave her as a child. Instead, it just reminds him of the war and Marco's death, making him feel awful. He doesn't open up to Lin, making Ruth furious at Thomas for his cold behavior.
Thomas goes to visit the Vietnam Veterans' Memorial in Washington D.C., along with several other men who served. This dredges up more disturbing memories of his time in Vietnam, as he mourns for all of the people he saw killed. While hanging out in a hotel room, Thomas notices the ring on his friend Dwight's finger. He recalls Dwight's past jealousy of him and his various nasty remarks. He realizes that Dwight is very likely the man who murdered Marco. He confronts Dwight about it and Dwight denies these claims. Thomas returns his medals to the Pentagon. He confesses to a military doctor that he killed the people in his platoon, but the man simply tells him to put the past behind him.
Thomas returns to Dark River and talks to Ruth, opening up about what happened to him in Vietnam. He tells her that he forgot his traditional values and became a man of war and violence. He tells Ruth about Dwight and killing the whale. She becomes angry when she learns that Marco did not want to hunt the whale but Thomas insisted. She blames him, in part, for what happened to Marco.
Thomas tries to return to his roots. He paddles a canoe into the water, with some other men, and starts singing ancient songs that have been passed down through generations of his tribe. Dwight sees Thomas and, sensing an opportunity, shoots him. Thomas seems to be dead, but Native spirits restore him, returning his life to his body. He convalesces on a nearby island and slowly returns to the way he was before the war. Dwight is arrested for Thomas's attempted murder. Thomas reconciles with Ruth and leaves for Vietnam, in search of Lin. The book ends with an image of the spirits restoring him.
