This is the story of Shed, a boy growing up in Idaho at the turn of the century. Shed, who believes he has a Native-American mother, is berdache, the Native-American third sex. Though physically male, he has feminine attributes and is bisexual. For the first half of the novel, Shed is trying to figure out who he is. He lives in a whore house run by Ida Richilieu, a bossy but deeply caring woman who acts as his mother. His own mother disappeared, hunting down a man who raped Shed. Shed later finds her body in the mountains.

One day he leaves Ida's place to visit his mother's people. On the way, he meets Dellwood Barker, a white man, who talks to the moon. Shed discovers a photograph of his mother in Dellwood's things and assumes that Dellwood is his father. Nevertheless, they fall in love and begin a sexual relationship. Dellwood believes in Moves Moves, the substance in sperm that gives life. The two separate so that Shed can go to the Indian reservation. He gets shot while there, but an old Indian man saves his life by breathing his soul into him.

Shed returns to Ida's where Ida, Shed, Dellwood (who stumbles back into Shed's life), and a whore named Alma Hatch, form a new family. Together they fight the racism and bigotry of the Mormons who take over the town. Ida and Alma get lost in a snow storm. Alma dies and Shed and Dellwood have to amputate Ida's legs which are badly frostbitten. They help her to heal by giving her the energy of their Moves Moves. By the end of the novel, Shed is content with his identity.