Although the plot of Pachinko chronicles the events of several generations of one family, the story focuses on Sunja, who is born in Korea and later moves to Japan with her husband. The novel opens before Sunja is born, describing the way her mother, who had grown up in dire poverty, had been “matched” to Sunja’s father, who had a cleft palate and a twisted foot, through the work of a local matchmaker. Sunja’s father, Hoonie, adored his daughter but died at the beginning of her adolescent years.

As a teenager, Sunja is captivated by an older man named Hansu. After becoming sexually intimate with him, Sunja realizes that she is pregnant. She is secretly pleased by the surprise and begins planning to move to Japan, Hansu’s home. When Hansu returns from a trip, Sunja reveals her secret and is horrified to learn that Hansu has a wife and daughters in Japan. He offers to give Sunja money and a house, and it is only at this point that Sunja realizes the dire social implications of her situation. While most families would not have “risked” having their sons marry a girl whose father had birth defects and could therefore genetically pass those along, they certainly wouldn’t consider a marriage to a woman who already had a child by another man. Realizing that she has jeopardized her mother’s modest business through her own impulsivity, Sunja becomes hopeless.

Around this time, a Presbyterian pastor named Isak passes through their small town, inquiring about lodging. His own brother had spent some time at Yangjin and Sunja’s boarding house years earlier, and Isak is hoping to stay there as well. He quickly falls ill, and Yangjin recognizes the signs of tuberculosis. After nursing him back to health, she shares the details of her daughter’s predicament. Isak offers to marry Sunja and to take good care of both her and the unborn baby.

After a modest wedding, Isak and Sunja move to Japan, where baby Noa is born. The family lives with Isak’s brother and sister-in-law, Yoseb and Kyunghee. Sunja and Kyunghee quickly become as close as sisters, sharing their dreams and challenges. Isak and Sunja add a son to their family and name him Mozasu. When Isak is imprisoned by Japanese authorities for supposedly failing to worship the emperor in a public ceremony, Sunja and Kyunghee begin a small business to support their family. While Yoseb refuses to allow his own wife to be seen working publicly, she is allowed to help Sunja prepare the food which will be sold at the market.

Years after the imprisonment, Noa returns home from school to find his father lying in the middle of the floor; his physical condition is so dire that Noa doesn’t even recognize him at first. Sunja tries to make Isak comfortable, realizing that the authorities have only released Isak because they don’t want him to die in prison. Isak dies after spending a short time with his family.

The women continue selling food at the market, and their business is given a tremendous boost when a man named Kim Chango hires them to cook for him instead of selling their food out of carts. He offers the women a substantial amount of money to prepare food for his restaurant, and they agree.

Near the end of the war, Hansu appears at the restaurant to tell Sunja that their town will soon be bombed. He has arranged to move everyone to the countryside and urges Sunja to protect her sons. Yoseb is conveniently offered a job in Nagasaki, and the rest of the family moves to a farm just before Osaka is bombed.

After studying for years, Noa is finally admitted to Waseda University, and Hansu offers to pay his tuition and expenses. The truth about his biological father is revealed when Noa’s girlfriend, Akiko, asks in a moment of personal fury for Noa to tell her the truth about Hansu. The physical resemblance, she points out, is obvious, and she is certain this is why Hansu pays for Noa’s expenses.

When Noa asks his mother about Hansu, Sunja is honest and tells her son the truth. Humiliated, Noa disappears to Nagano to begin a new life. He asks his mother to never contact him and begins identifying as a Japanese man. He marries and has four children while becoming a successful pachinko businessman; he always sends some money home to his mother but always uses different postmarks so that she cannot track him down.

Meanwhile, Mozasu drops out of school and begins working for a pachinko owner. Mozasu proves himself trustworthy and quickly gains status in the company. He marries Yumi, who works as a seamstress and whom Mozasu respects greatly. After they suffer several miscarriages, they have a son, Solomon.

Sixteen years after Noa’s disappearance, Hansu finally locates his son. When he takes Sunja to see him from a distance, she is overcome with emotion and jumps out of the car to greet Noa. Noa takes her into his office and briefly speaks with her, telling her that no one in his life knows the truth about his identity. Sunja is filled with relief to see him again, but moments after she leaves, Noa shoots himself.

Yumi dies after being hit by a car while walking with Solomon; witnesses say that she was able to push her son out of the way, likely saving his life. Mozasu eventually begins a relationship with Etsuko, a Japanese divorcee who feels that she has shamed her children by her infidelity. Hana, her only daughter, is the only child who still communicates with her. Solomon attends college in the United States, where he meets Phoebe. After graduation, she returns to Japan with him, but the relationship dissolves not long thereafter.

As Hana is dying, she encourages Solomon to work for his father in the pachinko business. Solomon believes that his father is an honest man, unlike his financial partners, and begins making plans to pursue that career path.

At the novel’s conclusion, Sunja visits Isak’s grave, recalling people whom she has loved and lost over her lifetime. She learns that Noa had faithfully visited Isak’s grave even while he was living in Nagano, thereby expressing his appreciation for Sunja and Isak’s sacrifices.