The plot structure of In the Lake of the Woods doesn’t follow a conventional path. The story jumps back and forth in time and setting, a structure reflected in this overview. Like a complex jigsaw puzzle, bits and pieces of information are presented to readers in an order that reveals information, a little at a time, to slowly uncover events and reasons why characters, John Wade in particular, act, think, and feel the way they do. At first, this structure may seem confusing, but as the novel moves along and readers put more and more pieces together, characters and events become clearer.

In a cottage by Lake of the Woods, an area that contains a huge lake located between Canada and Minnesota, John and Kathy Wade, a married couple in their late thirties, try to heal their wounds after John’s devastating primary election loss. They are both unhappy, each for their own reasons, but they spend their evenings on the porch, pretending to buoy themselves up with talk of a better future.

One day, John and Kathy drive into town and have a short argument at the Mini-Mart. Kathy thinks John blames her for his election loss. Later that night, they go to bed, and the next day Kathy is gone.

The book includes many “hypothesis” chapters, each presenting an idea of what could have happened. The first of these chapters suggests that Kathy got into a waiting car. The book also includes several chapters titled “Evidence.” These chapters present quotes from characters, snippets from books, and various exhibits, all of which provide readers with information that may or may not explain what happened to Kathy and why. Much of the evidence presented relates to John’s time in the Vietnam War.

When John is a teenager, his father commits suicide. John loves his father so much that he pretends he isn’t dead. As a child and teen, John also performs magic tricks.

In college, when John meets Kathy, he vows to use “tricks” to make her fall in love with him. John plans to become a politician, and he enlists in the Vietnam War. John’s platoon, Charlie Company, calls him “Sorcerer” because he does tricks and brings good luck. Two years later, he returns home. He spies on Kathy and discovers her being unfaithful to him. They marry anyway.

At the cottage, the night before Kathy disappears, John imagines fighting Jesus, and he kills houseplants with boiling water. He goes into the bedroom with the teakettle. John forgets what else happens. He wakes up alone the next morning. The next hypothesis presented is that Kathy heard John say, “Kill Jesus!” and saw him kill the houseplants, so she ran away in fear.

John embraces magic as a way to escape his father, an alcoholic who teases him mercilessly. John proposes to Kathy at a college bar. He writes Kathy from Vietnam but doesn’t tell her about all the death he sees. One morning in Vietnam, John is surrounded by machine-gun fire. He shoots at things including PFC Weatherby, a fellow soldier. Then he convinces himself it never happened.

Back at home, John and Kathy get married, and John becomes a state senator. For a while, John and Kathy are spontaneous and passionate. By the time he gets elected lieutenant governor, he and Kathy have marital problems. One night, John tries to talk to Kathy about Vietnam, but she deflects the conversation. John sometimes yells out in his sleep.

When John wakes up in the cottage bedroom without Kathy, he isn’t worried. He figures she’ll show up later. He does chores, makes plans, and drinks. At midnight, John goes to the cottage owner, Claude Rasmussen, for help. They decide they will call the authorities in the morning. The next group of evidence presented shares the recollections of Kathy’s and John’s friends and family.

Helicopters from John’s platoon set down in the village of Thuan Yen. Most of the soldiers brutally shoot the villagers. John doesn’t want to be part of it, but he kills an old man and Weatherby.

The next hypothesis presented is that Kathy, scared after finding the dead houseplants, takes out the boat and drowns.

The morning after Claude and John report Kathy missing, the county sheriff, Art Lux, and local police officer, Vinny Pearson, arrive and question John. An employee at the Mini-Mart says she witnessed an argument. John spends the night drinking with Claude. He is unable to reach Kathy’s sister, Pat, but Pat sees the news of Kathy’s disappearance on TV. Evidence presented next shares testimony of the soldiers who took part in the Thuan Yen massacre. Lieutenant Calley ordered the men to shoot everything.

When John returns home from the war, he successfully runs for state Senate with Tony Carbo as his campaign manager. John and Kathy spend their money on his campaigns and put off buying a house and having children. Kathy feels shut out from John. John has been elected lieutenant governor when Kathy becomes pregnant. He convinces her to get an abortion because of the bad timing. Kathy has the abortion but is upset as all she ever wanted was a baby. Four years later, John gives a speech announcing his run for the Senate primary. Kathy thinks he didn’t talk about issues enough, but Tony thinks image and winning are most important.

The next hypothesis shows Kathy in the boat heading toward the nearby town. She gets lost and eventually stops at an island for the night. Kathy thinks about a man named Harmon with whom she had an affair.

Pat arrives at the cottage to join the search. She distrusts John. They discuss John and Kathy’s relationship. John knew about Kathy’s affair, and Pat says that Kathy hated being a politician’s wife. The next collection of evidence includes how good John was at magic and fooling people.

The massacre at Thuan Yen continues all day. John tells PFC Richard Thinbill he killed two people. Calley orders the company to search and destroy the village. Sorcerer tells Thinbill they will have to forget this day, but Thinbill wants to report what happened.

John concedes early on the night of the primary because the election is a rout. Kathy is radiantly happy that John didn’t win. The next hypothesis picks up with Kathy on the island. She is back in the boat, but she is lost.

The next day John and Pat go out on a boat to search for Kathy with Claude. John has a hard time concentrating, which angers Pat. When they get back to the beach, they encounter other searchers. Vinny, who thinks John killed Kathy, and John argue, while Pat talks with the sheriff. They all continue to go out every day for several weeks but find nothing, and most of the searchers give up. John thinks about the magical art of making oneself disappear, which his father did with his suicide. He figures out how to make himself disappear too and dives into the lake. He resurfaces and later finds out the police are going to search the cottage next. John asks Claude for a boat because he wants to go out alone, but Claude refuses. John prepares himself, and the next morning he takes the keys to Claude’s boat.

The next hypothesis suggests Kathy committed suicide.

After Thuan Yen, John enlists for another year. He tries to drive the images of the murdered people out of his head. Before he returns to the United States, he takes a desk job, and he edits files to erase himself from his platoon.

The next hypothesis suggests that John kills Kathy by pouring boiling water into her eyes. Afterward, he throws her weighted body into the lake and sinks the boat.

On Claude’s boat, John motors into Canadian waters. Over the next few days, he calls out for Kathy and drinks. He uses the radio to broadcast himself speaking about Kathy. Then he throws the radio overboard and keeps going.

Law enforcement never finds any evidence of Kathy around the cottage. The mystery of what happened to her, and John as well, is never solved. Most people think they are somewhere else together. This is one possible hypothesis, according to the narrator.