Set in the 1920s, Tracks is the chronicle of the Anishinabe community in North Dakota and the struggle for land and the continuance of their tradition and beliefs that undergird the heterogeneity of their tribal society in the face of shifting U.S. policies. Told in the counterpointing voices of Nanapush, a tribal elder, and Pauline Puyat, a mixed-blood member of the community, the novel describes the intertwining lives of Fleur Pillager, Nanapush, Pauline, and their families; the horrible losses from epidemics, as well as the powerful love circulating among the community, and their resistance to cultural and political domination.

While these issues occupy much of the story, Pauline’s decline into an excessive and destructive religious asceticism is also a central part of the plot. Pauline’s internalized racism (she "would not speak our language" [p.14]) takes its shape in her hatred of her own body and her fascination with death ("I handled the dead until the cold feel of their skin was a comfort, until I no longer bothered to bathe once I left the cabin but touched others with the same hands, passed death on" [p. 6]). She ends up in a convent inventing new ways to torture herself as she listens to Jesus tell her she is not really Indian.

In contradistinction to Pauline are Nanapush and Fleur, who resist dominance and claim their identities in magnificent ways. In one scene, Nanapush refuses to allow a doctor to treat his granddaughter’s severely frostbitten foot with amputation, knowing that "saving [her] the doctor’s way would kill [her]." Nanapush nurses her himself, saving the foot and telling her stories as a way to walk her through the pain of healing.