The story is divided into ten parts.
Book One: Awake to Emptiness Bold and Psin, scouts in
Timur's army, discover a
Magyar city where all the inhabitants have died from a plague. Timur turns his army around and orders the scouting party executed to avoid the plague, but Bold escapes and wanders through the dead lands of Eastern Europe, encountering only one lone native. Upon reaching the sea he is captured by Turkish Muslim slave traders and sold to
Zheng He's
Chinese treasure fleet. Bold befriends a young African slave, named Kyu, whom he cares for after the Chinese castrate him. In China, they are kept as kitchen slaves until Kyu burns the restaurant and convinces Bold to escape with him. The pair make their way north to Beijing where they find work at the palace of
Zhu Gaozhi, heir to the
Yongle Emperor. The vengeful Kyu, hating the Chinese for what they have done to him, incites violence between the
eunuchs and the
Confucian administrative officials. After his scheming is discovered, Kyu is assassinated. Kyu and Bold reunite in the
bardo, where Bold explains to Kyu the concepts of cyclical reincarnation alongside one's
jati. He explains that their jati also includes Psin, the restaurant owners Shen and I-li, and an unknown number of others, and that their group has been especially close since an avalanche in Tibet killed them all at once in a previous cycle. Kyu resolves to do better in his next life.
Book Two: The Haj in the Heart In
Mughal India, two Hindu girls named Kokila and Bihari grow up together studying traditional medicine. Kokila is married to the son of an unpopular village headman. Her husband's brother gets Bihari pregnant, and Kokila is too late to save her from dying in a miscarriage. In revenge, Kokila uses her knowledge of herbs to fatally poison her brother-in-law and father. She is executed for her crime. Kokila reincarnates as a tiger named Kya, who saves Bistami, a
Sufi mystic of
Persian origin, from an attack by Hindus. After seeing Bistami beaten by his older brother, Kya kills the brother, and is trapped and killed by the villagers in retaliation. Bistami goes on to become a judge for the
Mughal Emperor Akbar, but later falls into his disfavour and is exiled to
Mecca. Bistami spends a year in Mecca before learning that he is being blamed for Akbar forsaking Islam, and departs again, traveling to the
Maghreb and
Iberia (Al-Andalus). Accompanied by Ibn Ezra, a follower of the historian
Ibn Khaldun, Bistami joins a caravan led by Sultan Mawji and his wife Katima, who seek to found a new city on the other side of the
Pyrenees. The caravan members found a city called Baraka on the abandoned former site of
Bayonne, France, and create a model society based on Katima's feminist interpretation of the
Quran. After Mawji dies, Katima rules the community on her own. Believing this to be heresy, the Caliph of Al-Andalus sends an army against Baraka. Bistami, Katima, Ibn Ezra, and their remaining followers flee again, this time founding the city of Nsara (near
Nantes, France).
Book Three: Ocean Continents The
Wanli Emperor orders a fleet under Admiral Kheim to invade Nippon (Japan). When the wind fails to arrive, the huge fleet is swept out to sea by the
Kuroshio Current and set adrift on the unexplored Pacific Ocean. Deciding that their only hope of returning home is to ride the
North Pacific Gyre, the fleet navigates all the way to the
New World. The sailors land on the West coast of North America and make contact with the peaceful
Miwok people. Kheim befriends a girl named Butterfly and begins teaching her to speak Chinese. Once Kheim discovers they have infected the indigenous people with disease, he orders his crew to leave at once, but a sailor named Peng jumps ship to remain with his Miwok lover. Butterfly comes aboard the fleet, intending to voyage with Kheim back to China. Continuing south, Kheim's fleet encounters the
Inca Empire. They are taken prisoner, and both Kheim and Butterfly are set to be ritually sacrificed; Kheim escapes by awing the natives with his flintlock pistol. On the return trip to China, Butterfly is fatally injured during a storm and soon dies. Kheim tells the Emperor that the Inca are militarily weak and rich in gold. In the bardo, a grieving and enraged Kheim attacks the goddess
Kali with his sword, but is unable to wound her.
Book Four: The Alchemist Khalid, an alchemist from
Samarkand during the
Bukhara Khanate, attempts to fool the Khan into believing that he has discovered the
Philosopher's stone. The Khan's aide discovers the fraud and Khalid's hand is severed as punishment. Khalid becomes disenchanted with alchemy and decides to destroy all his books. His friend Iwang, a Tibetan Buddhist mathematician, and son-in-law Bahram, a Sufi blacksmith, instead convince Khalid to test the claims in the books through practical experiments, particularly those of
Aristotle. Khalid and Iwang devote themselves to demonstrations that use the
scientific method to greatly progress knowledge of physics, chemistry, mathematics, biology, and weaponry. Their discoveries inspire Samarkand's other
madrasa scholars to conduct scientific investigations of their own. However, the Khan still sees Khalid as a con artist, and demands that he prove his worth by inventing new weapons to fight the rising Chinese threat to the East. The Chinese attack never comes; in the end, everyone at Khalid's lab is killed by an outbreak of plague, implied to have resulted from the Khan's refusal to listen to Khalid and Iwang's suggestions to improve the city's sanitation.
Book Five: Warp and Weft The
Iroquois people, referred to throughout by their own name of Hodenosaunee (People of the Longhouse) hold a ceremony to raise a foreigner named Fromwest to the rank of Chief. After distinguishing himself in a game of
lacrosse, Fromwest tells the story of how he came to the northeast of the continent he calls Yingzhou. Formerly a
samurai named Busho, he fled to the New World after the Chinese conquered Japan. He was eventually captured by a war party of
Sioux and rescued by warriors from the
Seneca people. In an ecstatic vision, Fromwest appears to remember his past lives. He realizes that Peng (from "Ocean Continents") made his way to the Hodenosaunee and taught them about
variolation, blunting the impact of
smallpox epidemics on their civilization. Fromwest reveals that he has come to organize the Hodenosaunee into a larger defensive alliance capable of resisting Chinese and Muslim colonizers, and offers to teach them how to mass-produce their own firearms. After their next deaths, the jati members apply scientific reasoning to the bardo, and manage to resist drinking the tonic of forgetting before being reincarnated.
Book Six: Widow Kang During the reign of the
Qianlong Emperor, Chinese widow Kang Tongbi takes in a Buddhist monk and his son whom she finds scavenging. The monk, Bao Ssu, is wrongly implicated in a series of
queue cuttings and dies in prison. Later, Kang meets a
Hui Muslim scholar named Ibrahim ibn Hasam, and they perform a ritual that allows them to remember their past lives. Kang and Ibrahim marry and move to
Lanzhou in western China, where they work to try to reconcile Islamic and Confucian beliefs. Kang anthologizes proto-feminist poetry and becomes a well-known writer. The
Jahriyya Islamic movement gains adherents in the west but faces intolerance from the Qing administration, leading to a revolt that the Qing crush with massive force. Lanzhou is swamped by a dramatic flood; Bao Ssu's son rescues a pregnant Kang from the rising waters. In a work based on Kang's ideas, Ibrahim publishes his thoughts on the Four Great Inequalities: warriors and priests over farmers, men over women, men over children, and certain races over other races.
Book Seven: The Age of Great Progress In the equivalent of the Christian 19th century, the Indian state of
Travancore has overthrown the
Mughals and the
Safavids and developed
steam engines,
ironclad warships, and
military balloons. Using these new weapons, they sail to
Kostantiniyye and easily topple the
Ottoman Empire. A Muslim Armenian doctor named Ismail ibn Mani al-Dir, who had served the Ottoman Sultan, is captured and sent to Travancore, where he happily joins the hospital of Travancore and works in anatomy and physiology. Ismail eventually meets their ruler, the
Kerala of Travancore, who aims to drive out the Muslim invaders and unify India—and eventually the whole world—into a democratic confederation. Later, during the
Xianfeng Emperor's reign, the Japanese enclave known as
Gold Mountain (in the real-world San Francisco Bay Area) has been subjugated by Chinese colonists. A Japanese slave named Kiyoaki is swept out to sea by the
Great Flood of 1862. Along with a pregnant Chinese refugee, Peng-ti, Kiyoaki manages to flee to the great coastal city of Fangzhang. There, Kiyoaki joins a Japanese freedom movement supported by Travancore, with Ismail acting as a liaison.
Book Eight: War of the Asuras Book Eight is set in the 20th century, during the "Long War". The world has become divided into four great alliances: the Chinese Empire and its colonies, the fractured Muslim world (
Dar al-Islam), and the democratic Indian and Hodenosaunee Leagues. At the outbreak of war, the Muslim states put aside their differences to fight the larger threat of China. The Indian and Hodenosaunee Leagues stay neutral at first, but eventually ally with China, seeing the Muslims as their greater enemy. The war drags on for decades and causes major changes in human society, including rapid industrialisation, mass conscription, and mass casualties. New devastating weapons and methods are employed, including
trench warfare,
chemical warfare, and air strikes. Chinese officers Kuo, Bai, and Iwa fight in the trenches of the
Gansu Corridor, where the ground has been blasted down to
bedrock by sixty years of bombardments. Kuo is killed when a shell penetrates their bunker. Bai and Iwa are ordered to move with their company south through
Tibet to support their Indian allies. At a pass in the Himalayas, they witness Muslim artillery destroying the top of
Mount Everest so that the tallest mountain in the world will be in Muslim lands. Bai is plagued by visions of his dead friend Kuo, who tells him that he is already dead, killed by the same shell that killed Kuo. After extreme difficulties, Bai and Iwa's forces manage to breach the Muslim defences at the pass. The Chinese army pours through to join forces with the Indians, turning the course of the war in their favor. The Chinese and Indian Buddhists unite to share a ritual beside the destroyed
Bodhi Tree.
Book Nine: Nsara In the aftermath of the Long War, a young Muslim woman named Budur and her aunt Idelba escape Budur's restrictive traditional family in the
Alps and move to the more liberal and cosmopolitan city of Nsara. They stay at a
zawiyya, a refuge for women, where Idelba restarts her work in physics and Budur enrolls in university to study history. She grows close to Kirana, a
feminist history lecturer who questions everything about Muslim society and argues for
emancipation and
liberation. The two have a brief affair. Life in Nsara becomes increasingly difficult as the Islamic world faces the effects of losing the Long War, including
hyperinflation,
food shortages, and
strikes. Many governments in Dar al-Islam are overthrown by coups. When the military attempts to overthrow the legitimate government of Nsara, Budur and Kirana incite mass protests. Eventually, the Hodenosaunee League send a fleet from their naval base at
Orkney to back the protestors in Nsara, forcing the military to surrender. Meanwhile, Idelba's work in atomic physics lead her to the disturbing discovery that it is possible to build a
devastating weapon from
nuclear chain reactions. The government learns of her work and raids the zawiyya, but Budur manages to hide Idelba's papers. Idelba dies of radiation poisoning and leaves all her research to Budur, who has begun using the principles of radiation to develop
Radiocarbon dating. Budur's work in archaeology gets her invited to an international conference of scientists in
Isfahan, Iran. There, she convenes a group of scientists from all the major world powers, all of whom agree to convince their various governments that nuclear weapons are too impractical to manufacture. The group initiates an international scientific movement to break down barriers between cultures. In the halls of the conference, Budur is overcome by an exhibit about a Tibetan village preserved by an avalanche, but cannot explain why.
Book Ten: The First Years Bao Xinhua is a revolutionary in China, who works under the leadership of his friend Kung Jianguo. Bao and Kung successfully overthrow the oppressive Chinese government, but Kung is assassinated on the cusp of their victory. Disillusioned, Bao leaves China and serves as a diplomat all over the world, eventually marrying and settling down to raise two children in Fangzhang (San Francisco). After his wife dies, Bao accepts a diplomatic post in
Myanmar, where he reunites with a comrade from his revolutionary years named Isao Zhu. Zhu poses many macrohistorical questions, attempting to arrive at a unified theory of history; in a moment of
Metafiction, Zhu and Bao contemplate using the bardo as a narrative device to illustrate the gradual improvement of human society. Bao later returns to Fangzhang to teach history in a village implied to be located near real-life
Davis, California. At the end of the novel, he meets a new student named Kali, implied to be Kung reborn. ==Style, themes and genre==