The whole story, told by the first person narrator Doc Hata, consists of flashbacks. The main story line begins from the time he gives up his store in Bedley Run until he meets his adopted daughter again. The sub story lines show the reader about his time during the war, and about his time with a teenage daughter and how difficult it was to raise her.
At the beginning of the story, Doc Hata describes his current situation and place of living. He lives in a small but affluent town called Bedley Run, where he is from the first accepted by the other inhabitants as a decent shopkeeper and later revered as the ideal citizen. His previous occupation is revealed to be that of a shop owner, as he formerly owned the pharmacy named Sunny Medical Supply, which he has sold to a young couple from New York. He has difficulty leaving his old life behind him and visits his old store nearly every day.
Liv Crawford is introduced, who is a real estate agent and wants him to move and sell his house. Doc Hata thinks a lot about his past in Bedley Run but also about his past experiences in Japan. He gives many insights into his daily routines, such as walking by his old store and going to swim every day in his pool. He thinks a lot about his daughter Sunny and how she arrived when she was a little girl. Later on, it becomes clear that Sunny was adopted and that Doc Hata specifically wanted to a girl, and even bribed the relevant person to get what he wanted. He remembers Sunny playing the piano and the initial problems he had with her.
In the first flashback we can see how he remembers his time with Mary Burns, one of his neighbors. He remembers meeting her the first time during his gardening. She quickly becomes a kind of girlfriend for him and spends a lot of time with Sunny, who does not accept her at all. Although Mary Burns works a lot on her relationship with Sunny, the young girl does not get along with her. In her first conversation with Doc Hata it becomes clear that he is not a real doctor, but that everybody calls him 'doc' because of his store. Mary Burns is very impressed by him because of the fact that he lives in a house that would fit a real doctor and his salary. At the beginning, the relationship between Doc Hata and Mary Burns is very close but they soon start to argue about Sunny and how Doc Hata treats her.
Doc Hata gives one piece of information about his daughter after the other, never giving all the information at the same point. While the story is going on it becomes clear that a big fight between Doc Hata and Sunny took place a while ago and separated them. During a stay in the hospital, where he has to stay for almost burning his own house, Doc Hata remembers what this fight was about. In hospital Officer Como's daughter visits Doc Hata and he begins to remember which problems Sunny had with Officer Como. Sunny was in trouble and she did not accept the authority of the police officer. This is just the beginning of the tragedy which is going on between Sunny and Doc Hata. At this point of the story, in the flashback situation, it becomes clear that Sunny runs away from home and that she meets with dubious persons.
Going on in the story, Doc Hata goes back in time a lot; he starts to talk about his time in World War II. He explains that most of the soldiers and also some officers had fun with abducted young women, who were brought there for the pleasures of the soldiers. He talks in particular about one girl he thought of the whole time.
He is determined to find Sunny again from the information given to him by a police officer. He also gives more background information on his conflict with Sunny. He encounters her in a mall, where failure of business is imminent in all the stores except for the one Sunny manages. She now has a son, named Thomas. Doc Hata tries to reconcile with Sunny by offering to help her take care of her son, whom Sunny is too busy to pay attention to. Sunny also expresses her need to find new ways of employment, as her store will be closing soon.
In a flashback, Hata focuses on his relationship with K. She is a sex slave (comfort woman) from Korea. Originally, Captain Ono expresses a peculiar interest in her, and Hata as well; Ono tells Hata that she is to be kept away from the comfort house, where the other comfort women are staying, and also tells him to inform everyone that she is sick, signified by a kurohata (black flag), to make sure that only he had access to her. K grows close to Lieutenant Kurohata, because they are able to talk to each other in her native tongue. The two speak frequently of their backgrounds, and it is revealed that K is from a higher-class family that did not value their daughters, resulting in her "volunteering" to become a comfort woman. Kurohata finds himself thinking about her frequently, growing more anxious to see her in the evenings every day. He falls in love with her intelligent demeanor and ethereal beauty. He is overcome with desire and has intercourse with her without her consent. Later, Captain Ono tells Lieutenant Kurohata that he is going to have sex with K, and when he reports this to K, she begs him to kill her, saying that if he truly did love her, he wouldn't naively think that they could live together after the war. Kurohata refuses. When Ono arrives and tries to have sex with her, she stabs him in the throat, killing him. She asks Hata to kill her too with Ono's pistol, but instead, he fires his gun at Ono's corpse and tells the others that Ono was showing off his gun and accidentally killed himself. In the end, Doc Hata does not say explicitly that K died after she is raped by 30 or more soldiers, but it is clear that she dies. He admits that he has frequent hallucinations of her in his house in Bedley Run, draped with a black flag.
Doc Hata eventually changes for the better and appears to move on from his traumatic experiences in the war. He and Sunny grow closer again, and he is shown selling his house.