The book opens with a psychopathic killer torturing and murdering Wendell Two Knives. Two Knives refuses to reveal where he hid Shiloh, a famous singer running from an enemy who wants to kill her.
Already two people, Shiloh’s mother and Shiloh’s psychiatrist, have been murdered. As a child, Shiloh saw her mother’s murder. Her psychiatrist may have helped her remember the episode and name the murderer.
A search party sets off into the Boundary Waters wilderness to find Shiloh. Along the way, they find out about Wendell’s murder.
Wendell’s ten-year-old grand nephew Louis guides the party. The party includes Aurora, Minnesota, former sheriff Cork O'Connor; two supposed FBI agents; Shiloh’s stepfather; and Wendell’s nephew (Louis' father) Stormy Two Knives.
Two men claim to be Shiloh’s father, a dying mobster and a well-known politician who is on his way to becoming governor.
All nature gathers to help save Shiloh. Amidst a series of brutal killings (including the murder of two innocent fishermen who cross paths with Shiloh), a gray timber wolf shadows Shiloh and protects her.
Cork O’Connor’s estranged wife Jo plays a crucial part in the story. She is the first one to figure out who is paying for the killing.
But at the heart of the story is the wolf and the idea of Wendell’s walk on The Path of Souls. The book portrays the evolution of Wendell’s hero story. It tells how heroes touch lives and save people in ways some cultures remember forever.
Boundary Waters ends with a moving scene where the youngest member of the search party, Louis Two Knives, tells Wendell’s hero story.