The novel opens in Hakodate, a port city in northern Japan, where Nagare Tokita speaks by phone with his deceased wife, Kei. Kei has traveled from the past to the Tokyo café Funiculi Funicula to meet their daughter, Miki, but a mix-up sent her fifteen years into the future instead of ten. Nagare chose to stay in Hakodate so Kei could spend her limited time with Miki. After hanging up, he enters Café Donna Donna, which, like its Tokyo counterpart, contains a chair that allows customers to travel through time.
The café's rules are strict: Nothing done in the past can change the present. The traveler can only meet people who have visited the café and must remain seated in a designated chair. The journey begins when coffee is poured and ends when it cools. The coffee must be poured from a silver heirloom kettle by a female member of the Tokita bloodline at least seven years old, and the traveler must finish it before it cools or become a ghost trapped in the chair. The chair is perpetually occupied by such a ghost, an old gentleman who vacates the seat only once daily.
Nagare has relocated from Tokyo to manage the café after his mother, Yukari Tokita, the owner, left for America. Accompanying him are his cousin-in-law Kazu Tokita, the waitress, and Kazu's seven-year-old daughter, Sachi, the only family member currently able to pour the time-traveling coffee. Reiji Ono, a part-time employee who dreams of becoming a comedian, rounds out the staff. Regulars include Nanako Matsubara, Reiji's childhood friend, and Dr. Saki Muraoka, a local psychiatrist. A motif threads through the novel:
What If the World Were Ending Tomorrow? One Hundred Questions, a book Sachi uses to pose hypothetical dilemmas to customers.
In the first story, a young woman named Yayoi Seto visits the café and mutters upon leaving that she would be better off dead. She drops a photo of a young couple with a baby alongside a much younger Yukari, dated that very day. That evening, Yayoi returns and reveals her parents were killed in a car accident when she was an infant. Orphaned and shuffled between relatives who treated her as a burden, she was placed in a children's home and spent years sleeping on streets and in internet cafés. She saved for a one-way ticket to Hakodate, intending to confront her dead parents and let the coffee go cold, becoming a ghost.
Sachi pours the coffee and Yayoi travels back roughly twenty years. She finds a young Yukari chatting with two aspiring comedians she recognizes as the now-famous duo PORON DORON. Minutes later, her parents, Miyuki and Keiichi Seto, enter with their newborn. As Yayoi watches with mounting anger, Miyuki tearfully thanks Yukari for saving her life at a pier years earlier, describing a past that mirrors Yayoi's: abandoned at four, passed between relatives, and driven to the brink of suicide. When Yayoi takes the family photo, she sees through the viewfinder the same image she has carried for twenty years and realizes she was always part of the family, cradled in her mother's arms. She drinks the coffee and returns.
Immediately after, the ghost transforms into a gaunt, dirt-covered woman: Miyuki herself, arriving from a time before Yayoi's birth, when she was suicidal. Yukari had placed her in the chair with vague instructions to picture the future she wanted. Kazu tells Miyuki the woman before her is her daughter. Yayoi abandons all resentment and fabricates a happy life, telling Miyuki she is twenty, lives in Osaka, and is getting married. Miyuki cradles Yayoi's face, promises to persevere, drinks the coffee, and vanishes, calling Yayoi's name beautiful as she fades.
The second story centers on Kohta Hayashida of PORON DORON, who has been visiting the café for three days. His comedy partner, Gen Todoroki, has gone missing since their victory at the Comedian Grand Prix, a prestigious comedy competition. Todoroki's wife, Setsuko, a childhood friend who supported the duo for years, died five years earlier; her dying words urged them toward the Grand Prix. Hayashida believes Todoroki will come to the café to see Setsuko. That evening, Todoroki arrives and travels to the past.
Moments later, Hayashida storms in, revealing Todoroki's text was a farewell: He intends to let the coffee go cold and become a ghost. In the past, Todoroki finds Setsuko and tells her they won the Grand Prix; she erupts with joy. Setsuko then reveals she already knows she is terminally ill and deduces she is dead in his time. When Todoroki confesses he does not plan to return, she tells him that as long as he remembers her, she lives in his heart, and that only he can bring happiness to "the dead me." She pushes the coffee toward him. Todoroki drinks and returns, telling Hayashida that Setsuko would not let him say it was over.
The third story follows Reiko Nunokawa, whose younger sister, Yukika, died two months earlier. Unable to accept the loss, Reiko has developed severe insomnia and hallucinations, repeatedly searching the café for Yukika. She has broken off her engagement to her fiancé, Mamoru. One evening during a thunderstorm, a power outage plunges the café into darkness and Yukika appears in the chair from the past. Yukika reveals she already knows she is dying and traveled to the future with one message: She wants Reiko to keep smiling, because what frightens Yukika most is not death but the thought of Reiko losing her happiness. Reiko promises, and Yukika vanishes just before the lights return. A postcard from Yukari reveals she orchestrated the meeting months earlier, specifying the exact date and time of Yukika's arrival before leaving for America.
In the final story, Reiji passes his long-sought comedy audition and departs for Tokyo. After his departure, Saki reveals that Nanako has been living with acquired aplastic anemia, a rare blood disease, for three years and has traveled to America for a bone marrow transplant after Yukari located a donor. Nanako left without telling Reiji, not wanting to burden him, but left a handwritten letter admitting she is scared and saying she can never be "someone like Setsuko."
When Reiji returns and reads the letter, he is torn between his career and his fear of never seeing Nanako again. Sachi silently approaches, reminding him of the book's central question: What would you do if the world were ending tomorrow? Reiji travels back one week to Nanako's last visit. Nanako acts casual, but when she quietly asks in a trembling voice whether something happened to her, Reiji realizes she has been masking terror. He blurts out an improvised proposal, telling her she becomes his wife. Nanako, laughing and crying, accepts the supposed inevitability. When Sachi asks the book's final question, whether he would choose to be born even if the world were ending, Reiji answers yes, saying he would be happy to live even for a single day because no one truly knows the future.
A postcard arrives showing Nanako smiling after surgery, with Yukari beside her. Several months later, however, Nanako dies when her body rejects the transplant. Years later, Reiji wins the Comedian Grand Prix on his fifth attempt, visits Nanako's grave on Mt. Hakodate, and leaves
One Hundred Questions with a wedding ring tucked inside. The novel reveals that the book was authored by Yukari Tokita. Its afterword reads: "We mustn't allow the death of a person to be the cause of unhappiness...people are always born for the sake of happiness."