Five year-old Carter becomes an orphan in the late 1920s, and after his parents pass away, he is given to his grandparents; his Grandmother is a full Cherokee, his Grandfather, part-Cherokee and part-Scot. Grandfather and grandson forge a very special and close relationship. Carter calls his Grandfather "Granpa" and his grandparents call him "Little Tree". They teach him about his Cherokee culture, and his ancestry, as well as farming, nature, love and the importance of the spirit. As he gets older, they also teach him how to make whiskey - not the kind you might find today in the liquor store, but clear whiskey made from corn mash, more familiarly known as moonshine. They are gentle, benevolent guardians, and they raise Carter with a firm hand, but with a great deal of love and tenderness. What they want the most for him is that he becomes a young man with an independence of spirit, and the courage to follow it.
The little family live in a dry stream bed known as a hollow. It is a remote place where Granpa runs a small but productive moonshine business, which is illegal, because this is the time of Prohibition, when the manufacture and sale of all alcoholic beverages was banned entirely. The family are essentially living off the grid, trusting the Cherokee, and the mountain people, but viewing outsiders with a deep sense of suspicion. One such set of distrusted outsiders, the government, forces Little Tree to attend an Indian Residential School; despite the fact that the name suggests a certain deference to the ways of the Native American people, the opposite was actually the case, and the schools were in fact set up with the goal of assimilating Native Americans into the European-American culture through education.
Little Tree hates school. The Christian missionaries who run it are prejudiced against the Indians, and have no understanding of their strong connection to nature and the places that are important to them and their ancestral culture. When Willow John, a friend of Little Tree's grandparents, visits him at the school, he sees a boy who is withdrawn and unhappy, and demands that he is allowed to leave.
We do not meet Willow John much more in the novel, until he nears the end of his life. He becomes sick and a traditional song is sung to help him leave this world and enter the next. Two years after Willow John's death, Granpa passes away after a bad fall leaves him in failing health. He reassures Little Tree that he will see him soon, because in his next life he will make it even better. This sentiment is echoed by Granma; when Little Tree is away from the hollow, she pins a note onto her blouse, telling him that it is time for her to go, but that she and Granpa will be as present and as tangible in his life as the wind in the trees. They will wait for him in the spirit world, and then all three of them will return and make their next life even better. Granma passes away whilst taking a nap in her rocking chair on the front porch.
Little Tree leaves the hollow after losing his grandparents. He takes Granpa's two hounds with him for company, and the trio head west. Little Tree works as he travels, earning food and lodging in return for his working on the farms that he stops at along the way. Little Red falls through ice on the creek, dying after becoming trapped in the freezing water. Blue Boy dies of old age a year later. On his own, Little Tree is now a man, and he uses The Way that his grandparents taught him as the framework for his life. It is part of him, like the wind blowing through the trees.
