Disgrace begins in Cape Town, South Africa with our narrator telling us that by this point in his life, 52-year-old Professor David Lurie has "solved the problem of sex rather well" (1.1). We learn that he gets his jollies out by visiting a prostitute named Soraya once a week, and that while he fulfills his desires with her, the sex is missing that "wow" factor. In fact, David doesn't feel much passion for anything in his life, from his love life, to his career, to his hobbies – until Melanie steps in, that is. David begins a slightly stalker-ish affair with Melanie, a student in his Romantics course, who awakens a passionate side of David that he didn't know existed anymore.
Things start to feel a little bit off with her almost immediately, though, and we start to get the vibe that their affair is pretty one-sided. It comes to an end when David finds out that Melanie has filed a complaint against David with the University. After an investigation, David loses his job, his status, and, as the title implies, his dignity.
Realizing that there's nothing for him in Cape Town, David opts for a change of scenery. He heads east across the country to the rural town of Salem in the Eastern Cape, where his daughter Lucy lives alone on a smallholding (a small farm that usually supports just one family – this word pops up a lot in the book), growing vegetables to sell at the Saturday market and running a kennel for dogs. David begins a new life there, helping Lucy at the market, assisting Lucy's neighbor Petrus with odd jobs and taking care of the dogs, and volunteering at the Animal Welfare Clinic with Bev Shaw. He also spends time poring over his newest academic project, an opera based on the love affair between the British poet Lord Byron and his mistress Teresa Guiccioli.
Things seem to be going just fine for a while, despite David's apparent distaste for the life that Lucy has chosen for herself. Lucy realizes that David would have expected a daughter of his to choose a more prestigious life path rather than, you know, digging around in the dirt all day by choice (rather than by necessity) and hanging out with unrefined, uneducated folks. Still, life in the country goes on without a hitch, and David seems able to adjust to it.
Then one day everything changes. David and Lucy are out and about taking a couple of the dogs for a walk when they run into three strangers – two men and a boy – on the road. Both David and Lucy feel a little sketched out by the encounter but shrug it off and keep walking. When they get home, they find that all of the dogs in the kennel are barking like crazy. The boy has apparently been taunting them from outside the pen while the two men (whom the narrator calls the tall man and the second man) just seem to be waiting for David and Lucy. The boy tells Lucy that they need to use the phone because the sister of one of the men is having an "accident" – that is to say, a baby.
Lucy tells David to stay outside while she takes the tall man indoors to use the phone. Big mistake. The second man runs in to the house behind them and locks David out. In a total panic, David lets go of the bulldog's leash and commands the dog to go after the boy. Then he kicks down the kitchen door. Apparently untrained in the going-after-bad-guys arts, David falls victim to the intruders almost immediately; he feels someone whack him over the head. He falls down, barely conscious, and feels himself being dragged across the floor.
When he comes to, he's locked in the bathroom and wondering what's going on with Lucy. The second man comes in to get the car keys from David and then locks him back in. Meanwhile, he looks out and sees the tall man with a rifle. The tall man starts shooting the dogs one by one, splattering brains and guts all over the place. And if that isn't bad enough, the second man and the boy come back in the bathroom, douse David with alcohol, and set him on fire (luckily just his hair catches ablaze and he extinguishes himself in the toilet). They leave, stealing David's car. David and Lucy are left to deal with everything that just happened. During this whole nightmare, Petrus is nowhere to be found.
Over the coming days and weeks, Lucy falls apart both physically and emotionally, and it's pretty clear that the men raped her. Still, she doesn't want to pursue the crime as a rape – she is only willing to report it as a robbery and assault (on David; not on herself). The relationship between David and Lucy grows increasingly strained, and David turns to Bev for advice over and over again.
Petrus comes back and throws a party at his place. David and Lucy attend, and things seem to be going all right until Lucy tells David that the boy is at the party and they have to leave. David gets all worked up and goes to confront the boy. Petrus gets in the middle of their fight, and it becomes pretty obvious that Petrus and the boy know each other pretty well. David says he'll go to the police. Lucy gets upset because she doesn't want David to ruin everything for Petrus, who is just starting to make his way in the world. Instead of making things better, David just ends up making things worse between himself and Lucy.
David tries to spend time outside of the house to give Lucy some breathing room. He spends more and more time with Bev in the clinic, helping her to put unwanted animals to sleep and taking whatever advice he can get from her. Somehow, in the romantic light of the clinic's surgery room, Bev takes a shine to David and they end up having sex on the floor.
Soon after, David gets a call that his car has been found and that arrests have been made in his case. He's pretty psyched – until he finds out it was all a mistake. This experience brings a lot of repressed emotions to the surface, driving Lucy and David's relationship to a breaking point. He realizes he has to leave.
On his way back to Cape Town, David goes to visit Melanie's dad to explain his side of the story. Melanie's dad invites him over for dinner with the whole family. It's awkward. David apologizes for what he put everyone through.
David arrives back in Cape Town and finds that his home has been robbed. He tries to start over, but realizes that what he wants to do is to come crawling back to Lucy. A phone conversation with Bev gives him the excuse to do just that: she tells him that there have been "developments" and that he should talk to Lucy.
David goes back to the Eastern Cape only to find out that Lucy is pregnant, and that it's likely that the boy is the father. Also, she's decided to keep the baby, which throws David for a loop. The next time he sees the boy (whose name, we find out, is Pollux), David gives him a good smack in the face.
As the novel ends, David is back in the clinic with Bev, once again putting animals to sleep. He picks out his favorite dog from the clinic's shelter and gives it to Bev, saying that he is "giving him up."