The Russian Aleuts land on the Island of the Blue Dolphins to hunt for otter. They negotiate with the natives, though they eventually break their promise. The Russian hunters kill many of the islander men, and then sail away.
The first stage of the novel sets up a typical conflict of cultures: two very different groups of people who don't get along so well (the natives and the Russians) are in one tiny location (the island) competing for resources (the otter pelts). What results is a bloody power struggle in which one group gains the goods (the Aleuts) and defeats the other group (the natives) in a dramatic battle. One of the major questions for the novel, then, is how can two very different groups of people – such as the Aleuts and the natives – learn to live together? Can two violent societies ever learn to get along? Since the leader of the islanders, Chief Chowig, is killed, it will be up to his daughter to figure out the answer to this big question.
The people of the island struggle to survive and eventually leave for the mainland. In the hustle and bustle, Karana's brother Ramo gets left behind. Karana selflessly throws herself off the side of the ship to return to him because she does not want Ramo to be left alone..
Typical roles get reversed when the social order of the island is wiped out after the battle. The women begin to take the roles of the men. What kind of new society will take the place of the old violent one that self-destructed? What happens next is that the society breaks apart (flees to the mainland) and all that's left is Karana and Ramo. It's now up to Karana and her brother to impose some sort of order on the island.
Ramo declares himself the new chief, though this is a joke in and of itself since he's a bit young for that kind of thing. Always brave, Ramo sets off by himself to sail in one of the left-behind canoes. He is killed by the pack of wild dogs that roams the island while he's out. Karana finds his body and vows revenge on the dog pack.
In this stage, the patriarchal order of the island is restored. (A patriarchy is a society ruled by men.) Ramo, the son of Chief Chowig claims his place as the new leader of the island. His bid for power, is of course a silly one. He's just a little boy, after all, and he's younger than his sister. Any hint of the old way quickly turns tragic as Ramo gets killed by the wild dog pack (they themselves a memory of the men who once lived there). It seems that the patriarchal society Ramo represents is doomed to self-destruct and must be replaced now. This task is up to Karana who is the only one left on the island
In this stage, Karana is haunted by memories of the past and tries to escape the island. Her canoe leaks during the journey, though, and she has to return home. Once back on the island, she's suddenly overjoyed to be there; she realizes the Island of the Blue Dolphins is indeed her home.
This part of the novel is about our main character struggling to be OK with her past. How can she live on this island with all the death and destruction that has come before? She is constantly reminded of the people who came before her, and the people she lost. Karana gets so lonely she tries to flee the island, but her boat soon springs a leak. Her defeat on the sea and return to the island shows that she has the humility needed for survival – something that Ramo, her father, and the Aleuts all lacked. Eventually, Karana returns to the island and is at peace with her life there until the white men return.
Karana confronts the leader of the wild dog pack and injures him. She nurses him back to health, rather than killing him, and the two become friends. Karana also comes into conflict with a number of animals on the island (the sea elephant, the devilfish) some that wound her, some that she wounds, and some become her friends. She eventually adopts an attitude of peacefulness toward the animals.
In this section, we watch Karana struggle with her attitude toward nature. Will she seek bloody revenge on the leader of the dog pack, and continue the cycle of violence, or will she try something else? Fortunately, Karana decides not to kill the dog and nurses him back to health and becomes his buddy. Here, we see the destructive warlike tendencies of her culture being replaced by Karana's care of others. This pattern will repeat as Karana makes a bunch weapons for her defense and offense, and then faces many of the islands more dangerous animals. After she befriends a sea otter and its children (suggesting a circle of life rather than a cycle of death), she decides never again to commit an act of violence against an animal.
The Aleuts come back to the island. Karana hides in a cave and is eventually discovered by an Aleutian girl named Tutok. The two girls trade gifts and words, and become friends.
Karana has come to terms with the natural world and even became friends with the dog that killed her brother. But, she must now reconcile herself with the culture that killed her dad. Will forgiving the Aleuts be as easy as it was with Rontu? Hardly. Karana is scared of the Aleuts and hides from them. It's only after young Tutok extends a gift of friendship that Karana attempts to understand this other culture. The two girls become good friends, enjoy each other's company, and teach each other the words of their own languages (trust and communication is key). Their friendship is short, but represents a hope for the possible mending of the break between the two cultures.
The white men finally return to the island and take Karana to the mainland. She gets to bring her dog and birds with her, but they make her put on a neck-to-toe dress.
The conclusion of the novel leaves us with a bit of a cliffhanger: what will Karana's life be like on the mainland? Will the attitudes she developed on the island still apply when she gets to shore? A clue to that answer is given to us when Karana is measured for the dress that will cover her body. This perhaps suggests that Karana will be forced to assimilate to the ways of the white men on the shore. Or will she?