The main character is a girl named Karana. She has a brother named Ramo, whose curiosity usually leads to trouble. Her people live in a village called Ghalas-at and the tribe survives by means of gathering roots and fishing. One day, a ship of Aleuts led by a Russian named Captain Orlov arrive and persuade the natives to let them hunt sea otter in return for other goods. However, the Aleuts attempt to swindle the islanders and leave without paying. When they are confronted by Karana's father Chief Chowig, a battle breaks out and lives are lost on both sides. The tribe is greatly reduced and the Aleuts leave the island leaving little payment for the otters they hunted. Karana's father and many other men in the tribe die during the battle.
Later, the "replacement chief" Chief Kimki leaves the island on a canoe for new land in the East. Eventually, he sends a "giant canoe" to bring his people to the mainland even though he himself does not return. The white men come to Karana's village and tell them to pack their goods and go to the ship. Karana's brother misses the ship to retrieve his fishing spear. Although Karana urges the captain to wait for Ramo to return, the ship must leave before a storm approaches. Despite restraint, Karana jumps off the ship and swims to shore and the ship departs without them.
The siblings live alone on the island, hoping the ship will return. However, Ramo is brutally killed by a pack of feral dogs. Alone on the island, Karana takes on traditionally male tasks, such as hunting, making spears, and building canoes to survive. She vows to avenge her brother's death and kills several of the dogs, but has a change of heart when she encounters the leader of the pack. She tames him and names him Rontu (meaning "Fox Eyes" in her language).
Over time, Karana makes a life for herself. She builds a home made of whale bones and stocks a cave with provisions in case the Aleuts come back, so she can hide from them. As she explores her island, Karana discovers ancient artifacts and a large squid (which she calls a devilfish). As time passes, she decides to hunt the devilfish. She also tames some birds and an otter while feeling a close kinship to the animals (the only inhabitants of the island beside herself).
One summer, the Aleuts return and Karana takes refuge in the cave. She observes the Aleuts closely and realizes that a girl named Tutok takes care of the domestic duties including getting water from the pool near Karana's cave. Fearful of being discovered, Karana goes out only at night yet the curious girl stalks Karana and the two meet. Karana and Tutok meet several days in a row. However when she lets Rontu out with her, Tutok calls him hers. Karana and the girl exchange gifts and she realizes how lonely she's been. Karana wishes that Tutok would not leave yet the next day Karana makes food for her and she doesn't come and Karana sees the ship departing. Sadly, she returns to her house and starts rebuilding.
More time passes and Rontu dies. Karana soon finds a young dog that looks like Rontu and takes him in naming him Rontu-Aru ("Son of Rontu"). One day, Karana sees the sails of a ship. It docks at the shore, but then leaves. Two years later in the spring, the boat comes back, so Karana dresses in her finest attire and goes to the shore to meet the boat. Her rescuers see that her dress made of cormorant feathers is not appropriate for the mainland and they have a dress made for her. Although she does not like the dress, Karana realizes that it is part of her new life. The ship takes Karana and Rontu-Aru to the mission in Santa Barbara, California. There, she finds out that the ship that had taken her people away had sunk before it could return from the mainland for her.