The novel is narrated by twelve-year-old Karana, who belongs to a small tribe of Native Americans living on the island of Ghalas-at, off the coast of California. She is the daughter of Chief Chowig, and is very close to her family, which includes her older sister Ulape and her six-year-old brother Ramo.
One day, Karana and Ramo spot red sails on the horizon while they are out gathering roots. The red sails belong to the Aleuts – Native Americans from Alaska - who are led by a Russian, Captain Orlov. They have come to Ghalas-at to hunt otter so they can sell the pelts back on the mainland.
Captain Orlov negotiates an agreement with Chief Chowig. He and his men will be allowed to camp on the island and hunt otter if they give the tribe half of the collected pelts. Karana is upset by the negotiations for two reasons. The first is that her father told Captain Orlov his secret name. (In Karana’s tribe, everyone has two names – one for everyday use, and a secret one to be used only on special occasions.) The second is that she does not want the Aleuts to kill the otter, who are beautiful and fun-loving creatures. The tribe is also worried because the Aleuts dealt unfairly with them in the past.
When it is time for the Aleuts to leave, they only offer one trunk of spearheads and jewelry, and no pelts, despite the fact that they have had a very successful hunt. Chowig demands three more trunks, but the conflict leads to a full-scale battle between the Aleuts and the tribe’s warriors. The Aleuts win because they have a cannon, which they use to kill many of the warriors. More than half of the tribe’s members die in the battle, including Chief Chowig.
After the Aleuts leave, only fifteen people are left in the tribe – and none of them are able-bodied men. Everyone has to do double duty to survive, and the new chief, Kimki, eventually sails to the mainland in hopes of finding a place for the tribe to relocate.
After several months, Kimki sends some white men to bring the rest of his tribe to the mainland. Because the weather is stormy and it is difficult for ships to anchor near the island, the tribe packs quickly and rushes. Nobody notices that Ramo has run off to get his spear until they are rowing towards the ship in canoes. When the others refuse to turn back for him, Karana dives into the water to rejoin Ramo. Together, they watch the ship leave.
Karana and Ramo believe that the ship will return for them soon, but it is not long before food shortages become a problem for them. The wild dogs that roam the island have already eaten much of the food that the tribe left behind, so the children must use their fishing and gathering skills to survive. Even so, they find their situation fun at first – especially Ramo, who proclaims himself Chief of Ghalas-at. But only a few days into their stay on the island, the wild dogs kill Ramo when he sneaks off alone to the place where the canoes are tied up.
Karana is devastated by her brother’s death. She buries him in a cave and vows to kill the wild dogs. She also burns down her village because it reminds her too much of Ramo and the rest of her family. To protect herself from the wild dogs, Karana makes herself a spear, a bow, and arrows. This is an important decision because women are not supposed to make weapons in Karana's tribal culture. Though worried she will be punished for it, she makes the weapons nevertheless because she has to protect herself. She also sets up her camp on a large rock near the beach because it is protected from the dogs.
Months go by, and the ship does not return. As winter nears, she decides to attempt an escape herself, and modifies an old canoe so that it is small enough for her to manage. She takes it to Santa Catalina, the nearest island. Unfortunately, the boat starts to leak after she has been rowing for a full day and night. She turns back, worried she will die but encouraged by a group of dolphins who swim beside her as she travels back to Ghalas-at.
The failed escape attempt changes Karana’s perspective on her situation. She accepts that the island is her home, and tries to focus on the good things about her new life. She also stops trying to escape, instead building a permanent house and a fence near a spring. Along with new cooking and fire-building skills, she ensures herself enough comfort that she can focus on avenging Ramo by killing the wild dogs.
Karana spends weeks preparing bigger weapons with which to battle the dogs. She works on them late into the night by the light of the sai-sai – tiny flammable fish that she uses to fuel her fires. She even attempts to kill a sea lion because their teeth make excellent spearheads. However, she fails because even the smallest animal is too big to kill with her arrows. In the attempt, she gets caught in a fight between two animals and wounds her leg so badly that she has to stay inside her house for five days.
It is during this period that she discovers a cave, which she decides to make into a second home. She can tell from the paintings and debris inside that it was used by her ancestors. Many days later, she notices that one of the sea lions has died, and she is able to harvest the teeth after all.
Knowing that she lacks enough arrows to kill all of the wild dogs, she focuses on the leader of the pack, a huge gray dog that she believes came from the Aleut ship. She smokes the dogs out of their cave, and manages to wound the gray dog and kill several others. However, when she finds the injured gray dog, she elects to nurse him back to health instead of killing him. After he recovers from his wound, he continues to hang around her house, so she names him Rontu and adopts him as a pet.
Rontu provides excellent company for Karana, and she realizes that she was incredibly lonely before she adopted him. However, she still worries that the Aleuts will return and hurt her. To prepare for this, she creates a small canoe from one of the tribe's old ones, so she can escape if necessary.
On a test ride around the island, Karana discovers a sea cave, which she decides to use as a hiding place for her canoe and her emergency supplies. As she is rowing out, pleased with her discovery, she and Rontu spot a giant devilfish – that is, a squid. Because the meat of the devilfish is so delicious, Karana decides that her next project will be to hunt and kill the enormous animal. To do this, she builds a spear with a long string attached, which she can throw over long distances and then reel in.
One day, Rontu returns to the wild dogs, which saddens Karana. One day, after several unsuccessful attempts to kill the devilfish, she discovers Rontu fighting with the two dogs who now lead the wild pack. She chooses not to intervene, and watches Rontu win the battle. He then returns to Karana, and the pack never bothers him again.
When she is not hunting devilfish, Karana passes the time by adopting songbirds as pets and making beautiful clothes and jewelry for herself. She eventually gives up on the devilfish and focuses on hunting abalone, a staple food for her people. But one day, when she least expects it, she manages to spear the devilfish. Both Karana and Rontu are injured, however, in trying to drag the strong squid to shore, and Karana decides that the meat is not worth the effort.
One day, she is exploring in the canoe when she finds what she calls Black Cave, a sea cave on the remote side of the island. Inside, she is frightened to find skeletons and dolls, presumably left there by her ancestors. When the tide rises before she and Rontu can paddle out of the cave, they are forced to spend the night there.
One day, the Aleuts return to the island. Before fleeing to her cave to hide, Karana notices that they have brought a young girl who does chores while they hunt. Karana remains hidden while the sun is out, but one day steps outside to admire a skirt she made. While outside, the Aleut girl surprises her. Although Karana is afraid at first, she and the girl slowly become friends. She learns that the girl’s name is Tutok, and even picks up a few words in Tutok’s language.
Karana still worries Tutok will betray her to the Aleut men, but is convinced to trust Tutok when the latter girl leaves a beautiful black necklace at the entrance to Karana's cave. Over the following days, the girls grow closer, teaching each other words. Karana even tells Tutok her secret name, and gives her a hair ornament made out of seashells.
One day, Tutok and the Aleut ships are gone, and Karana is once again alone.
The Aleuts leave behind many wounded otter, and Karana adopts one, whom she nurses back to health in a tide pool. She names him Mon-a-nee, which means "Little Boy with Large Eyes." After bad weather prohibits her from catching him fish for three days, she finds he has left the tide pool and returned to the ocean.
She consoles herself by adopting other pets, including an injured gull and the children of her two songbirds. Later in the year, she spots Mon-a-nee in the water with two pups and realizes that Mon-a-nee is actually a girl. She renames the animal Won-a-nee, which means "Girl with Large Eyes" and they become friends, playing together whenever Karana goes fishing in her canoe. Karana’s relationship with Won-a-nee and her pups inspires her to stop hunting animals. She lives off of fish, and uses plants for other necessities like clothes and building materials.
One summer, Rontu dies. Consumed with grief, Karana gives him a beautiful funeral and stops tracking how long she has been on the island.
Eventually, she decides to adopt a new dog, and chooses a wild dog who resembles Rontu. She tames him by drugging the entire pack, kidnapping him, and keeping him in her house until he becomes her pet. She names him Rontu-aru, which means "Son of Rontu."
Karana misses her friends and family deeply, but she has managed to make a secure life for herself on the island. But everything she has built falls into danger when an earthquake and a tsunami come to Ghalas-at. Karana is on the beach repairing her canoe when the tsunami hits, and she just barely escapes the large wave. She avoids a second, larger wave by clinging to the cliff side. The flooding leaves her stranded for the night. Only a day later, an earthquake damages her house.
Karana is rebuilding her wrecked canoe when she spots a ship on the horizon. Unsure whether the approaching men will be dangerous, she hides until they find evidence of her presence and call out to her. When they do, she rushes instinctively towards them, ready to return to civilization. Unfortunately, the weather is bad, and they are already in canoes heading back to the ship. She calls out, but they cannot hear her over the sound of the wind.
Two years later, the men return. This time, they stay long enough for Karana to change into her best clothes and gather her things. The men welcome her into their camp, although they make her wear new, uncomfortable clothes.
When they finish hunting, they take her to the ship so she can go to the mainland. She brings her favorite clothes and jewelry with her, as well as two songbirds and Rontu-aru. As the ship sails away, she looks fondly back and the island but is hopeful that her future will be even happier.