The novel is split into three parts.
The novel begins with Michael K, a poor man with a cleft lip who has spent his childhood in institutions and works as a gardener in Cape Town. Michael tends to his mother who works as a domestic servant to a wealthy family. The country descends into civil war and martial law is imposed, and Michael's mother becomes very sick. Michael decides to quit his job and escape the city to return his mother to her birthplace, which she says was Prince Albert.
Michael finds himself unable to obtain the proper permits for travel out of the city so he builds a shoddy rickshaw to carry his mother, and they go on their way. Soon after escaping, Michael’s mother dies in a hospital. He lingers for some time, carrying his mother’s ashes around with him in a box. Finally, Michael decides to continue on his journey to Prince Albert to deliver his mother’s ashes. Along the way, though, he is detained for not having the required travel papers, thus being assigned to work detail on a railway track.
After his job on the railway track is finished, Michael makes his way to the farm his mother spoke of on Prince Albert. The farm is abandoned and desolate. Soon, Michael discovers how to live off the land. However, when one of the relatives of the real owners of the farm arrives, he treats Michael like a servant. Michael dislikes this treatment so he escapes up into the mountains.
In the mountains, Michael goes through a period of starvation while he becomes aware of his surroundings. In his malnourished state he finds his way down to a town where he is picked up by the police and is sent to work on a work camp. Here, Michael meets a man named Robert. Robert explains that the workers in the camp are exploited for cheap labor by the townspeople. Eventually, there is an attack on Prince Albert and the workers of the camp are blamed. The local police captain takes over and Michael escapes.
Michael finds his way back to the farm but soon feels claustrophobic within the house. Therefore, he builds a shelter in the open where he is able to watch his garden. Rebels come out of the mountains and use his garden. Although Michael is angered by this he stays in hiding. Michael becomes malnourished and delirious again because he has not come out of hiding. He is found by some soldiers and is taken to a rehabilitation camp in Cape Town. It is here that Michael is identified as "CM," an abbreviation most likely signifying "colored male."
At the rehabilitation camp, a doctor becomes interested in Michael. He finds Michael’s simple nature extremely fascinating and finds him to be unfairly accused of aiding rebels. Michael becomes very sick and delirious because he refuses to eat. The doctor tries to understand Michael’s stubborn ways while attempting to get Michael released. However, Michael escapes on his own.
Upon his escape, Michael meets with a group of nomadic people who feed him and introduce him to a woman who has sex with him; later we see him attracted to women for the first time. He returns to the apartment where he and his mother lived in Cape Town, the same apartment and city he had tried to escape some time ago. Michael reflects on the garden he made in Prince Albert.
Some commentators notice a connection between the character Michael K and the protagonist Josef K. in The Trial by Franz Kafka. The book also bears many references to Kafka, and it is believed, "K" is a tribute to Kafka.