When the air raid sirens go off, Sarah, a schoolgirl in England, runs home to help her stepmother, Veronica, prepare the living room to protect the family from nuclear fallout. Sarah and Veronica assemble living provisions, rudimentary sanitary supplies, and clothes and toys for Veronica's son William (aged five) and daughter Catherine (aged seven). The family then shelter inside as the bombs fall.
Sarah realises that the water the rest of the family has been using has become contaminated with radioactive particles from the unblocked chimney, and all apart from Catherine are likely to contract radiation sickness. Veronica displays symptoms first and leaves the house several times to collect canned (safe) food for Catherine. She tells Sarah that community members have gathered in the church and a local farmer is giving away contaminated meat for free.
Later, when her symptoms become worse, Veronica leaves, presumably to die. William also begins to suffer from radiation sickness, and when he is near death and Sarah begins to weaken she leaves the house, bundling Catherine up against contamination. She gathers food for her from the house of the town farmer and takes her to the remote home of Johnson. Johnson has been prepared for the war, and appears unaffected by radiation sickness. During the time of the nuclear fall out Sarah has to take on the role as a mother due to Veronica saying that she is going to give up but Sarah refuses to let Veronica give up on herself.
This section begins with a flashback to the day of the war, which reveals that Sarah's father, Bill, a lecturer at Bristol University, was driving to a meeting when a woman named Erica flagged him down. As a leading authority on cellular cloning, she had a pass granting her (and anyone accompanying her) shelter in a government bunker. Bill takes Erica to the bunker at Avon, but had mixed feelings about surviving when his wife and children did not.
Within two months of the war, Britain is gripped by a nuclear winter. When the nuclear winter finally ends, the authorities send helicopters on reconnaissance missions, which reveal that against all odds, there are people still alive outside. They also learn that the ozone layer has been damaged, so anyone who goes outside must wear protective clothing.
Erica feels it is her duty as a woman still of child-bearing age to help repopulate society, so she marries Bill and gives birth to a daughter, Ophelia. Bill is assigned to teach the bunker's teenagers, and, though he is officially meant to teach science-based subjects, introduces subjects such as English literature and politics into the curriculum.
Ophelia spends the first sixteen years of her life in the bunker, where she calmly accepts the restrictions on her life. But other youngsters, in particular an Anglo-American youth named Dwight Allison, are not so accepting. Under the influence of Bill's teachings, Dwight has come to believe that General MacAllister, the man in charge of the bunker, has too much authority and, one day, spray-paints a slogan denouncing MacAllister as a "fascist pig". As a punishment, Dwight is sentenced to a year of hard labour and expelled from school.
Some time later, a large herd of cattle is found in one of the outside communities. MacAllister orders Dwight's father, Colonel Jeff Allison, to bring the cattle to the bunker for "government protection". Dwight believes it would be wrong to take the cattle when the outsiders depend on them for survival and hurries to tell Bill. Bill and Dwight decide that the best course of action would be to leave the bunker and warn the community which owns the cattle; Ophelia accompanies them, but she does so because they are the people she is closest to, not because she feels they are doing the right thing.
Outside, the world is recovering from the effects of the war and Ophelia is able to experience things she has previously only known about via her father's lessons. They discover the cattle owners are Johnson's community, and Bill is soon reunited with Catherine, who is heavily pregnant with her eighth child. She married Johnson when she was in her teens, but six of the children she has already given birth to have died in infancy due to genetic mutation. Since Johnson is old enough to be Catherine's father, Ophelia is disgusted, thinking the outsiders are uncivilised compared to the people in the bunker. Dwight retorts that the latter are like "dinosaurs", attempting to maintain pre-war standards of living and not adapting to the changed conditions in the world.
During the course of the day, Ophelia meets Catherine's only surviving daughter, Lilith, who was born with white eyes and pale hairs all over her body.
Since there is no other community which can handle a herd the size of Johnson's, Bill and Dwight are unable to get the cattle away before Colonel Allison and his men come to collect them. Johnson attempts to compromise by offering Colonel Allison enough cattle to form the basis of a herd, but Colonel Allison says he is not in a position to negotiate. Realising the discussion is going nowhere, Dwight sabotages all but one of the Army trucks, making it impossible to take the cattle back to the bunker, and escapes into the wilderness.
Ophelia wants to return to the bunker, even though doing so means she will never see Dwight again. The section ends with Ophelia in tears, as Lilith (with her newborn sister in her arms) smiles at her pityingly.
Five decades after the war, the bunker is decaying and fuel supplies have run out, and the people in the bunker have been forced to seek sanctuary among outside communities.
On one such expedition, Ophelia's son, Simon, sees a pack of wild dogs stalking a person who is searching the ruins of an old house. He fires his gun, killing one of the dogs and scattering the rest, then goes to help the person they were stalking. proves to be a mutant girl named Laura, who tells him that "weapons are evil" and that he has no right to kill a living thing. When Simon sees that Laura's body is covered with hair (which protects her skin from being damaged by ultra-violet radiation), he is repulsed by her, thinking she is an "ape".
Shortly after meeting Laura, Simon injures his leg on a rusty nail. Since his people have no means to treat injuries, he is taken to Johnson's community, where Laura lives. Rather than having separate homes for each family, the community consists of a large "house" which reminds Simon of a Tibetan monastery. Seeing the well-ordered community where people have learned to make everything they need themselves, Simon begins to feel that his own people are "failures", having tried to restore pre-war standards at the expense of their children's futures.
Simon meets Catherine, now known as "Blind Kate," blind after years of exposure to ultraviolet radiation and covered in festering sores. Simon sees in her a glimpse of his own future and, on learning that she is Laura's grandmother, is so repulsed at the thought of being related to a mutant that he can't bring himself to acknowledge it. Instead, when Laura asks if he has ever heard of the people who once came to the community to take the cattle, he claims not to know them.
The next morning, Simon finds himself the topic of much discussion among the mutants. Unable to bear being the subject of pity, he storms out of the dining hall and, following a vitriolic lecture from blind Kate, leaves the settlement even though his leg is not fully healed. He plans to catch up with the rest of his party, but a pack of dogs chases him into a ruined church. While there, he sees a glider flying overhead. The glider's pilot alerts Laura's people to Simon's whereabouts.
Laura rides to the rescue on her horse and uses her psychic powers to send the dogs away. She tells Simon that she and the rest of the mutants have developed telekinetic powers and the ability to communicate telepathically. She believes the mutants are a new species of humans, but they need the technical knowledge Simon's people have kept alive if they are to reach their full potential.
Simon comes to terms with what his ancestors did to the world and realises that, though he can't change the past, he can do something positive with his own life by helping his people collaborate with the mutants. He comes to believe that the nuclear war was meant to happen, so that Laura (whom he finally acknowledges as his cousin) and the rest of her kind could be born. Catherine initially acknowledged Ophelia who she met during the cattle mission,but Simon denied any knowledge of her. However at this point he finally admits to Laura that he is in fact her son. Laura was angry at first for Simon lying to her and denying an old woman the pleasure of meeting another family member, but then comes to terms with the situation. She takes Simon on her horse back to the house where he will reveal all and use his knowledge to allow the new generation to expand their skills and make the new way of life a better place.