Tracks alternates between two narrators: Nanapush, a jovial tribal elder, and Pauline, a young girl of mixed heritage. In Nanapush’s chapters the point of view is that of Nanapush telling stories to his granddaughter, Lulu, several years after the main events in the novel occur. When Lulu was ten years old, her mother, Fleur Pillager, sent her away to a government school. Because of this, Lulu is now estranged from Fleur. Nanapush, therefore, attempts to reconcile mother and daughter by telling Lulu about the events between 1912 and 1924 that led Fleur to her decision.
Nanapush first meets Fleur in 1912 when he rescues her in the middle of winter and nurses her back to health from consumption – a recent epidemic among the Anishinaabe. Because of their shared grief at losing so many from their community, Nanapush and Fleur develop a friendship and begin to see one another as family. The next year, Fleur goes to the nearby town of Argus and takes a job at a butcher’s shop, where she meets Pauline Puyat – the novel’s second narrator. After beating a group of men from the shop one night at a game of poker, Fleur is beaten and raped. She leaves town, but the next day a tornado strikes Argus. Mysteriously, no one in town is harmed in the storm with the exception of the men who raped her – whose bodies are found locked in the freezer of the butcher shop, where they had taken refuge.
Fleur returns to her family home on the reservation, where she meets Eli Kashpaw while hunting in the woods one day. Much to his mother’s dismay, Eli falls in love with Fleur and moves in with her. Soon, Fleur begins to show signs that she is pregnant and, although the true paternity is unknown, Eli takes responsibility of the child as his own. A new family unit begins to form at the Pillager home – Fleur, Eli and their daughter, Lulu, as well as Eli’s mother, Margaret, and her second son, Nector. Throughout the novel, Margaret and Nanapush, whom Fleur regards as a father, also develop an intimate relationship. Together, the family faces trials of hunger, tribal conflict, and ultimately the loss of their land to the government.
In the meantime, Pauline has also left Argus and is staying with a widow named Bernadette Morrissey, from whom she learns the art of tending the sick and dying. Pauline serves as a midwife to Fleur and begins to spend time at the Pillager home. She becomes increasingly jealous of Fleur and her relationship, and in an attempt to break them up, feeds a sort of love potion to Eli and a younger girl named Sophie, inducing them to copulate passionately in the forest. Claiming to have received a vision, she decides to join a convent, where she only delves further into obsession. She devotes herself to the cause of converting Fleur and the others, but is generally regarded as a nuisance. She develops several unusual habits as a means of self-inflicting suffering to remind herself of Christ’s suffering. Her behaviors are frowned upon by the superior nun and she is eventually sent away to teach at a Catholic school. Pauline's narratives deal with her own personal story and also provide a second perspective on many of the same events described by Nanapush.