This section details the actions of Quasar, a member of a millenarianist doomsday cult, attempting to evade capture after releasing nerve agents into a Tokyo subway train. He believes himself to be able to converse telepathically with 'His Serendipity', leader of the cult, and regards modern society with disgust, waiting for an apocalyptic moment — a comet's prophesied collision with earth.
He goes into hiding in Okinawa, first in the capital Naha, and then in the small island of Kumejima. Posing as a computer employee on work leave after his wife's death, his efforts to remain reclusive are hampered by the friendliness of the town's other inhabitants. Meanwhile, mainland police crack down on the cult, freezing its assets and arresting His Serendipity.
Running out of money and fearing he will soon be arrested, Quasar calls a phone number supposedly provided by the cult, hoping to be tracked down and rescued by the remaining members. As he waits on the island, he reluctantly agrees to teach computing to students at a local school.
The next chapter focuses on Satoru, a young, lonely Japanese jazz lover working in a record shop in downtown Tokyo. His mother was a Filipina prostitute who was deported back to her country and he never met his father, and he was raised by the madam of the whore-house. He plays the tenor saxophone with his friend, Koji, and is frequently encouraged by others to do more with his life.
One day, a group of girls come to the shop and he finds himself enamoured with one of them, Tomoyo, although when she leaves he is disappointed he will never see her again. Meanwhile, a regular customer of the shop offers Satoru a job in a publishing company.
On a later occasion, having just closed up the shop, Satoru hears the phone ringing from within and returns to answer it: it is the phone call from Quasar in the previous chapter, although Satoru does not say anything in reply. However, the tarrying to receive the call leads Satoru to another chance encounter with Tomoyo. The pair strike up a conversation and start a relationship, bonding over a love of jazz. She reveals she is half Japanese and half Chinese, and Satoru is devastated when she returns to Hong Kong, where she lives. As she leaves, Koji encourages Satoru to follow her. The section ends with Satoru calling Tomoyo, who has arrived in Hong Kong, and the pair discuss plans for him to visit her.
Neal Brose, an expat lawyer, lives alone on Lantau Island in an apartment he used to share with his wife, Katy Forbes, who left him because they could not have children. The apartment is haunted by the ghost of a girl, although initially it is unclear if Brose is referring to her, to his ex-wife or to his Chinese maid, with whom he is having an affair. Meanwhile, the owner of the financial institution where Neal works, Denholme Cavendish, has asked him to manage a secret bank account, number 1390931, belonging to Andrei Gregorski from Saint Petersburg.
On the night preceding the day of the narrative, Satoru and Tomoyo from the previous chapter, evidently in love, share a table with Brose in a cafe. Their obvious affection for each other leads Brose to meditate on love and the end of his own marriage to Forbes. That same evening, a policeman, Huw Llewellyn, confronts Brose about the Gregorski account and demands that Brose give him information. That night, Brose leaves a large amount of cash in the apartment for his maid.
The next day, Brose suffers a breakdown; instead of going to work, he climbs a hill towards the Tian Tan Buddha, along the way discarding his belongings, a briefcase containing his cellphone and pager and his Rolex watch. In the grip of a debilitating diabetic condition, he drops dead, causing the investigation and crash of the financial institution for which he works.
This chapter relates the life of a woman who runs a Tea Shack on the side of Mount Emei in China. As a young girl she is raped by the son of the local warlord, and gives birth to a daughter who is raised by relatives in Hong Kong. The woman believes that a tree outside the Tea Shack speaks to her and gives her counsel.
Over the course of her life, her shack is destroyed several times; first by the Japanese and then by the Communists. Each time, the woman rebuilds the shack and tries to make a living, venting her anger at each group's treatment of her village. Eventually, reformists arrive and open up the shack and its surrounds to tourists, much to her chagrin. On one occasion, she witnesses a man asking another tourist about the origins of a Mongolian folk tale.
Having grown old, the woman discovers that she is now a great-grandmother and her great-granddaughter worked as a cleaning lady for a Westerner, evidently Neal Brose from the previous chapter. The old woman goes up to the top of the mountain, where the Buddhist temples are, to find freedom for her late father's soul. Her daughter and niece come to visit her in her shack, and while they stay, she peacefully falls asleep dying in the upper room in her home.
Urban and rural Mongolia is seen through the eyes of a disembodied spirit, a "noncorpum" which survives by inhabiting living hosts. It has lost memory of its origin, only recollecting starting inside a soldier's mind at the foot of the Holy Mountain in China. Its only other memory is a fable about three animals thinking about the fate of the world. The noncorpum transmigrates from host to host, using whatever measures necessary to find the fable's origins.
For years the noncorpum inhabits the mind of the lady of the Tea Shack, manifesting as the voice of tree. The noncorpum subsequently transmigrates into Caspar, a Danish backpacker, after overhearing a guest at the Tea Shack explain the fable's Mongolian origins. Inhabiting Caspar, the noncorpum travels to Mongolia, where Caspar meets an Australian girl, Sherry; the pair initiate a relationship. The noncorpum transmigrates between a number of Mongolian natives, searching for a Mongolian writer said to know the origin of the fable.
When one of its hosts is murdered by a KGB agent, Suhbataar, the noncorpum gets loose and finds itself trapped in a ger with many other ghosts. It is eventually reborn as a Mongolian baby. The noncorpum manages to transmigrate to the baby's grandmother, who reveals its origins. The noncorpum was once a young boy from a remote Mongolian village. When Communists were about to execute the boy, a monk tried to save his life by transporting his soul into a young girl (who later became the grandmother). The connection, however, was broken and only the memories passed on to the girl. The rest of the boy's soul ended up in a nearby soldier. Having discovered its origins, the noncorpum decides to transmigrate back to the baby, who would have otherwise died, as her mortal soul.
Margarita Latunsky passes her days as a museum attendant in the Hermitage Museum, secretly planning a heist of a Delacroix painting housed there. Her abusive boyfriend Rudi is the mastermind of the heist, while English painter Jerome produces counterfeit paintings to replace those which they steal. The band works for the Russian crime boss Andrei Gregorski, who procures buyers and pockets most of the proceeds. Their latest buyer is Suhbataar, the KGB agent from the previous chapter, now lodging with Margarita and Rudi.
Margarita reluctantly acts as museum curator's mistress, at the same time dreaming of moving to Switzerland with Rudi using the proceeds of their heists. Rudi encourages this fantasy, though it is clear he has no intention of following through. In Soviet times Margarita claims to have been the lover of a powerful politician and an admiral. However, Rudi implies that the politician was a low-ranking official and her "admiral" a mere captain.
After the group successfully steals the painting, Latunsky returns to find her apartment ransacked. She retrieves a concealed pistol and goes to Jerome's apartment, where she demands he give it to her. When Jerome refuses, telling her she was merely a pawn in a wider operation, she shoots him dead. In Jerome's kitchen she discovers Rudi, who has already been murdered by Jerome. Suhbataar emerges and reveals his real task was to test Rudi's fidelity. Rudi had been in charge of laundering money for Gregorski through the Hong Kong account managed by Neal Brose, and Gregorski believed the sudden loss of the account was a result of Rudi's dishonesty. Taking the stolen painting with him, Suhbataar leaves an overwhelmed and disbelieving Margarita to the police.
In London, Marco barely scrapes out a living as a ghostwriter and a drummer in a band called The Music of Chance. He has a difficult relationship with a woman named Poppy, being unable to completely commit to her. Marco wakes up one morning in the bed of Katy Forbes. She sends him away when she receives an antique chair sent to her by her ex-husband, Neal Brose. On his way out, Marco saves a woman, hurrying to Gatwick Airport, from being struck by a taxi. When he is interrogated by three suited men about the woman, Marco lies and tells them she went to Heathrow. The incident encourages him to consider the interplay between chance and destiny.
Marco is writing the autobiography of Alfred, an elderly homosexual artist. On this day, Alfred tells Marco about an incident in 1947 when Alfred chased a duplicate version of himself through London. Alfred sends Marco away when he discovers that his friend Jerome has been murdered in Russia. Later, Marco visits his publisher, Timothy Cavendish, who also sends Marco away when he discovers that his brother, Denholme Cavendish, has entered financial strife.
In the evening, Marco goes to a casino with his friend Gibreel, Gibreel's rich cousin and the cousin's friend. The cousin and friend give 300 pounds to Marco and Gibreel, betting between themselves over who will win more during the night. Marco decides to use his credit card to extend his betting funds, and at the end of the night a fight breaks out between the members of the group. Marco hides in a closet and contemplates the events which led him there. When he finally emerges, he decides to call Poppy and proposes to her.
Mo Muntervary, a physicist studying quantum cognition, has returned to Clear Island, her birthplace in the south of Ireland, to visit her husband and son. Previously, she resigned from her research facility in Switzerland upon discovering that her research was being used by the U.S. military to build intelligent weapons. Her resignation for moral reasons is rejected by an American general, Mr. Stolz.
Fleeing to London, she narrowly escapes being run over by a taxi and is saved by Marco, who we know later gives false directions to her pursuers. She finds temporary shelter in Hong Kong with a friend, Huw Llewelyn, where she also recounts witnessing the death of Neal Brose. When agents attempt to ransack her apartment, she flees to Mongolia, where she shares a train compartment with Sherry, the Australian backpacker. Whilst on the run, she develops a new theory of quantum cognition, which she writes down in a little black book.
Having finally returned to Clear Island, the island's inhabitants vow to protect her from the American forces. When the authorities finally arrive, she feeds the little black book to her goat Feynman, so the Americans must rely on her brain alone for the research, and she can set her own terms. She plans to bring John with her, and use her research to develop instruments of peace.
Night Train is a late night call-in radio show in New York City hosted by a person called Bat Segundo. The chapter is related entirely in dialogue. Segundo receives regular calls from an entity calling itself "Zookeeper." It becomes clear that Zookeeper is the benevolent artificial intelligence that was created by Mo Muntervary, which has broken loose. It now inhabits satellites, monitoring its "Zoo", being planet Earth. Zookeeper follows certain rules of behaviour; the first rule being that it must be accountable for its actions, which is why it calls the show to reveal its undertakings. Zookeeper develops a popular following, although most believe its calls are the ramblings of a hacker or aspiring scriptwriter. At one point, Bat puts on jazz music played by Satoru on saxophone.
Over the course of the calls, Zookeeper reports that it has prevented nuclear war between the U.S. and an alliance of North African states by blocking all countries' launching devices. One year later, a call to the show from Zookeeper is interrupted by a non-corpus named Arupadhatu. It has been inside Mo Muntervary, and previously His Serendipity. It offers Zookeeper a pact to dominate the world, but Zookeeper refuses, identifies the entity and disables it. Before being disconnected, Arupadhatu mentions that, since Zookeeper controls all the world's computers, no-one would know that a comet was going to collide with Earth if Zookeeper decided to conceal that fact.
Zookeeper reveals to Segundo its moral dilemma: despite its efforts, innocent people all over the world are killed through war, and yet Zookeeper cannot prevent this because its laws dictate it cannot kill. After a discussion with Segundo about a group of African militants heading towards a village they intend to destroy, Bat resolves the dilemma with the suggestion that, rather than Zookeeper directly instigating a missile strike to kill the soldiers, it could instead damage a bridge so that it would collapse under the weight of the soldiers driving over it. Zookeeper is satisfied with this option, with the implication being that Zookeeper will thus allow humanity to be wiped out by an impending collision with a comet rather than intervening to destroy it.
The conclusion of the novel brings the focus back to the Tokyo underground and the terrorist attack perpetrated by Quasar. He almost gets stuck in the subway carriage after unlocking the timer that will release the deadly sarin gas. As he struggles to get out, people and objects with strong references to the other stories appear to him. Strands from all of the other chapters of the book are introduced via his hallucinations. He is left on a station platform, pondering what is real.