The novel is set in South Africa in the time of apartheid and civil war. Michael K is born with a harelip, and that and his seemingly simpleminded nature make his mother, Anna K, despair. She decides he should not be in regular school and sends him away to Huis Norenius, a place for “unfortunate” children. When K graduates, he becomes a gardener, living a quiet and solitary life.
Anna works as a servant for a wealthy family in Cape Town. She sees her situation as fair and her employers as kind, but her life grows more and more difficult when she gets very sick. She cannot do her job anymore and K has to come and take care of her.
Cape Town is full of unrest. Soldiers prowl the streets; beggars and the unemployed try to make do as the civil war and the concomitant military rule upend day-to-day existence. Anna cannot stop thinking about where she grew up—Prince Albert, in the country. She tells Michael he should quit his job because he will probably get laid off anyways, seeing how the economy is faltering, and they should return to Prince Albert. K acquiesces. He sets about obtaining the proper permits and secures a train reservation.
Unfortunately, the permits never come and the city is engulfed in more turmoil. K decides that he and Anna ought to leave by the roads; he can push her in a barrow with a roof that he has constructed since she is too old and sick to walk. Anna agrees, and the two set out.
Along the way, Anna dies of her illness. K is given her ashes and a set of clothing from the hospital staff and is on his own. He journeys throughout the countryside, pausing to sleep in the fields and under trees. The roads are filled with convoys and K tries to avoid them.
At one point, K encounters a barricade near the road; when the police discover he has no papers, he is seized and put into a forced labor gang. He works with other men breaking up obstructions on railway tracks.
When he is let out of his service, he resumes his journey to Prince Albert. He asks a shopkeeper for the location of the farm of the family his mother remembered. The shopkeeper suggests the Visagie farm but says they haven’t lived there for a long time. A boy gives K directions to the farm and he heads there.
The farm, located at the base of rolling hills with mountains beyond, indeed seems to be abandoned. K establishes a home of sorts after overcoming a brutal bout of sickness, and he finds joy in starting a small garden near the dam with seeds he discovers in the pantry. Unfortunately, his time here is short-lived when a young deserter from the military appears and says this is his grandparents’ farm and he needs to hide out here. He treats K like a servant; K does not want to live like that, so he leaves.
K seeks out a cave in the mountains. There, he grows weaker and weaker from lack of nutrition. His body revolts and he knows he is going to die. He comes down from the mountain and is picked up by police. He is taken to a hospital, where he recovers.
When he has recuperated, he is taken to a rehabilitation camp called Jakkalsdrif. He does not know why he is there and resents being there against his will. A man named Robert befriends him and tells him this place is not so bad because the men, women, and children here have beds, food, and work.
K grudgingly works and earns small wages, most of which he gives to Robert and his family. He suffers from ill health and decides he does not want to want to work anymore. He comes to understand Robert’s perspective: although there are basic necessities here, the people in the camp are despised by those on the outside and are essentially meant to be forgotten or eradicated.
K decides to leave the camp after the police punish the inmates for their supposed involvement in a fire in town. He returns to the Visagie place, which seems to be abandoned again. He constructs a hidden burrow in the small slopes near the dam, disguising it so that it cannot be seen from above or close-up. He begins planting again, spreading out his crops a bit and carefully limiting his irrigation so no one will see the contrasting verdancy of the area.
He has a great deal of peace here with his garden and his idle hours, but he is still constantly worried about people finding him. One night a group of men who live in the mountains and are considered rebels and brigands by the government because they will not participate in the civil war or allow themselves to be put into the camps, stay near K’s place. He hides himself in his burrow, but briefly considers joining them.
K’s health worsens. He is very weak and his head spins. He does not know if he is in possession of his faculties. Soon, he is discovered by the police. They question him, thinking he is a vagrant at first—but when they espy his burrow and supplies, they assume he is part of a network of resistors and criminals. The police blow up the property and take K away.
Part Two of the novel is narrated by a nameless doctor at Kenilworth, a rehabilitation camp. “Michaels,” as he is known at Kenilworth, is struggling to survive because he refuses to eat the food at the camp. The doctor is fascinated with him and comes to believe that he is not actually a part of the war but rather a strange and enigmatic figure who does not belong in the camp.
The doctor grows frustrated that Michaels will not cooperate and heal. Michaels is ambivalent about the doctor’s attention and seems merely to want to be left alone. He does not talk very often, but he does give some cryptic information about his overbearing mother. The doctor looks out for Michaels as much as he can, even putting the police at bay with a false report about his supposed participation in the mountain gang.
Michaels runs away; the doctor wishes he had been courageous enough to anticipate Michaels’s departure and subsequently follow him. He is unhappy here in this camp in this senseless war; he thinks that maybe, if he’d gone with Michaels, he could have found a place to live simply.
In Part Three, the narration shifts back to K, who has returned to Sea Point, Cape Town. He has no shoes and only overalls; he knows he looks like a beggar and will hopefully elude capture.
K is trying to get up enough courage to enter his mother’s former flat. In the meantime, he falls in with a few companionable but scurrilous men and women, and he is uncomfortable around them, especially when one of the women, a prostitute, performs fellatio on him.
K is still ill and has trouble keeping liquids and solids down. He is happy, though, to be free of the camps and to be on his own once more. He does not care that he is “simple,” and he knows the camps have not changed him.
He finally enters his mother’s former place, which looks now as if it were just storage for outdoor furniture and decor. He finds evidence that another vagrant is staying here, and he hopes this person, whom he sees in his head as an old man, will be pleased to find K here. This old man will be wanting a guide for the roads, and they can set out together.