The book begins with Indigo and Sister Salt, her sister. The two girls are part of the Sand Lizard Clan, a tribal group in Arizona, United States. A nearby town is very against the tribal ways of the clan, and whenever a child runs to them, they will torment them because of their culture. At times, it is said that the townspeople have killed Indian adults because of their ways.
The ways of this clan are very peaceful and ritualistic. The dunes in Arizona are the perfect source for water and food, and many of the children play there every day. The children are often sent there to retrieve materials to make new clothes and blankets. However, they must be very careful, because if any authorities were to find them there, they would be sent right away to a boarding school.
The novel is then broken into pieces when the sisters are separated when the authorities find Sister Salt. She escapes the police, but is recaptured and sent to prison. The police also take Indigo, who is sent to a boarding school as punishment. There, she is tormented, like her sister, for her race and identity. In the town, their mother grieves, but continues to work in the hot outdoors just to survive.
Things begin to look a bit brighter when Edward Palmer meets Indigo in the boarding school. He is impressed by the resilience she displays against the torment people bring her, and plans to adopt her. Just days later, Indigo becomes an official part of a white family that nurtures her.
The family moves around a lot, and through these moves, Indigo gets attached to Edward's wife, Hattie. The two become like best friends, and help Edward on his treks through the jungles of Europe and South America as he works as an anthropologist.
Indigo has now become a young woman, and decides to go back to the sand dunes where she grew up to look for her family.
