The novel is set in the American Northwest. The main character is Mackenzie Philips, a father of five, called "Mack" by his family and friends.
Four years prior to the main events of the story, Mack takes his three youngest children on a camping trip to Multnomah Falls and Wallowa Lake near Joseph, Oregon. Two of his children are playing in a canoe when it flips and almost drowns Mack's son. Mack is able to save his son by leaving his youngest daughter Missy alone at their campsite. After Mack returns, he sees that Missy is missing. The police are called, and the family discovers that Missy has been abducted and murdered by a serial killer known as the "Little Ladykiller". The police find an abandoned shack in the woods where Missy was taken, but her body is never found. Mack's life sinks into what he calls The Great Sadness.
At the beginning of the book, Mack receives a note in his mailbox from "Papa", saying that he would like to meet with Mack on that coming weekend at the shack. Mack is puzzled by the note - he has no relationship with his abusive father, who left when Mack was young. He suspects that the note may be from God, who his wife Nan refers to as "Papa".
Mack leaves his family and goes alone to the shack, unsure of what he will see there. He arrives and finds nothing, but as he is leaving the shack and its surroundings are supernaturally transformed into a lush and inviting scene. He enters the shack and encounters manifestations of the three persons of the Trinity. God the Father takes the form of an African American woman who calls herself Papa, Jesus Christ is a Mideastern carpenter, and the Holy Spirit physically manifests himself as an Asian woman named Sarayu.
The bulk of the book narrates Mack's conversations with Papa, Jesus, and Sarayu as he comes to terms with Missy's death and his relationships with the three of them. Mack also has various experiences with each of them. Mack walks across a lake with Jesus, sees an image of his father in heaven with Sarayu, and has a conversation with Sophia, the personification of wisdom. At the end of his visit, Mack goes on a hike with Papa, who shows him where Missy's body was left in a cave.
After spending the weekend at the shack, Mack leaves and immediately is nearly killed in an automobile accident. After his recovery, he realizes that he did not in fact spend the weekend at the shack, but that his accident occurred on the same day that he arrived at the shack. He also leads the police to the cave which Papa revealed, and they find Missy's body still lying there. With the help of forensic evidence discovered at the scene, the Little Ladykiller is arrested and put on trial.
