The novel begins with Brian Robeson, a thirteen-year-old boy from New York City, in a small bush plane on his way to visit his father in Canada for the summer. His parents recently got divorced, which has shaken him up, primarily because of the Secret that he keeps: he saw his mother with another man while his parents were still married. In the middle of the flight the pilot has a heart attack and dies, and Brian is alone; he tries to steer the plane for a little while but has no clue where he is and cannot get in contact with the ground. When the plane finally runs out of fuel, he makes a crash-landing in the middle of the forest beside a remote lake.
Brian survives the crash and, still trying to piece together what has happened to him, begins the long struggle for survival until he is rescued. The first few days are a blur as he recovers from the crash and tries to get his bearings. He remembers the motivational words an old teacher once said to him and decides to make the most of what he has and try his best to stay alive, hoping a plane will be there to rescue him within a couple of days. His most valuable tool is a hatchet that his mother gave to him before he left New York.
The first task is finding food. He first finds a patch of strange cherries, but eating too many of them makes him very sick. He then finds a raspberry bush and uses this as his first food source. He makes a crude shelter in a hollowed out part of a rock outcropping beside the lake; however, on his first night in the shelter a porcupine sneaks in, tries to eat his raspberries, and then sticks him with its quills. Frustrated and hurt, Brian reminds himself that he will not get anywhere by continuing to feel sorry for himself.
He discovers how to make fire by striking the hatchet against the stone and allowing the sparks to catch on a small nest of kindling. This fire gives him hope. The following day he finds a nest of snapping turtle eggs to use as an additional food source. He constantly gathers wood to keep his fire going, and when he is not gathering wood, he is gathering berries to eat. He begins to see the world differently, his thoughts, hearing, and vision in tune with the world around him.
But he needs another source of food, because the berries and the eggs will run out. He realizes that there are hundreds of fish in the lake for him to catch if he can figure out how; first he tries to make a fish spear with his hatchet and then a bow and arrow, but he cannot seem to spear any of the fish because they move too fast for him. While he is trying to spear them he suddenly hears a plane fly by, and attempts to light his signal fire in time for it to see. The plane disappears before he can manage this, however, and Brian realizes that now that the search plane has not found him here, it will not come back. He is extremely depressed, and wishes to die.
The novel flashes forward 47 days; Brian is now thriving in his forest haven, catching fish and birds for food. He is a new person now, determined and optimistic. He thinks back to the weeks that have passed and recounts major milestones that he has reached. He first managed to catch fish when he realized that water refracts and he actually had to aim below the fish in order to spear where they really were. He figured out how to shoot the birds and rabbits that live by the lake in order to have meat. But he made mistakes and experienced hardship, too: one night a skunk came into his shelter and stole his eggs, spraying him; out of nowhere a moose attacked him while he was in the lake, nearly killing him.
Eventually a tornado rips through his campsite, destroying everything, and he must start over. But he is the new Brian, so he does this with grace, quickly replacing everything he has lost. The winds brought the tail of the crashed plane up from the depths of the lake, and Brian remembers the survival pack inside of it. If he can get to the plane and get inside, he can get the survival pack with all the food and tools he could need. He makes a raft to use to get out to the plane and swims to it, using his hatchet to hack off the aluminum fuselage of the plane in order to get inside. In the process he drops the hatchet and has to swim down into the lake to retrieve it. He makes it inside the plane and gets out with the survival pack, but not before seeing the remains of the dead pilot, eaten by fish.
The survival pack has many spoils, including food, an emergency transmitter, and a gun. Brian feels strange about the gun, feeling as though it disconnects him from nature in some way. He sets out to make himself a feast out of the food, and then all of a sudden a float plane lands on the lake. It is a pilot who heard his emergency transmitter signal and came to rescue him.
The epilogue covers bits of Brian's life after his rescue. Things go back to normal, though the way his mind works has certainly changed. His parents at first appear to be getting back together, but this does not happen, and their separation persists. Brian never tells his father about the Secret.