Divided into four parts, Before the Coffee Gets Cold takes place entirely in Funiculi Funicula, a basement cafe in Tokyo that possesses magical properties and can transport customers backward or forward in time. The book opens with Fumiko and Goro, a couple who both work in medical IT, breaking up over coffee. Goro has just informed Fumiko that he is late for a plane to America, where his dream job awaits.
A week later, Fumiko returns to the cafe and relates the story to Hirai, the woman who runs the hostess snack bar next door, and Kazu, a waitress at the cafe. Fumiko asks to travel back in time. Kazu explains that no matter what she does while in the past, it won't have any effect on the present. She can also only meet people who have also visited the cafe. Finally, there is a time limit: you must finish your cup of coffee before it gets cold. The penalty for not returning in time is that you will become a ghost, replacing the ghost woman who sits reading a novel in the cafe's single time-travel seat. Kazu has no explanation for the rules.
Too impatient for the ghost to leave her seat to use the toilet, Fumiko grabs the woman's arm. The ghost curses Fumiko, paralyzing her in place until Kazu offers the woman a refill of coffee. Meanwhile, a nurse named Kohtake arrives to collect Fusagi, her husband. He has been sitting in the corner making notes in a travel magazine. Fumiko overhears that he is waiting to travel back in time. She is relieved when Kohtake convinces her husband to go home for the day.
Fumiko falls asleep while waiting for the seat to become available. The narrator comments on how she and Goro started dating after she was impressed by his talent as a programmer. She knew early on that his dream job was working for his uncle's gaming company in America.
Kazu wakes up Fumiko, giving her a chance to get in the seat. Kazu pours coffee, the steam of which blurs the bounds of Fumiko's reality until she is suddenly one week in the past. Although she wants to beg Goro to stay, she can't quite bring herself to say it. She scolds him for not having consulted her about his decision to leave. He admits that he always assumed she would leave him for a more attractive man, pointing to the large burn scar on his forehead. She shouts that it never bothered her. Goro asks her to wait three years for him to return. Fumiko returns to the present reassured to know that, while she hasn't changed her present, she may have changed her future.
In the second part, Hirai's sister, Kumi, visits the cafe, hoping to speak with her sister. She leaves a letter with Kei, one of the cafe owners. Hirai then reveals she has been hiding behind the counter to avoid her sister, who she believes resents her and wants her to return to Sendai to run the family inn so the sister can be free of the obligation. Hirai asks Kei to destroy the letter.
Kohtake, a nurse, arrives and addresses her husband, but he doesn't recognize her. Kohtake becomes upset, but she tells Kazu and Kei she knew this day would come; she is resigned to looking after him as a nurse would. Kazu informs Kohtake that Fusagi wants to travel back in time to deliver a letter to her. Kazu is convinced it is a love letter. Kohtake decides to travel back in time to a period when Fusagi still recognized her; then he could give her the letter.
Kazu pours the special coffee, which transports Kohtake back in time. Fusagi recognizes her when he enters the cafe. He notices the seat she sits in, and casually mentions that she is from the future, which must mean that she knows about his condition. Fusagi has the letter with him. Kohtake lies to Fusagi, telling him that his condition improves and he gets better. He says that she can get rid of the letter in that case.
Kohtake finishes her coffee before it goes cold and returns to the present. Kazu reads the letter aloud for her. In it, Fusagi asks her not to treat their relationship as one of nurse and patient. He would prefer for her to leave him. Kohtake leaves the cafe with a renewed affection for her husband, resolved to continue to treat him as such, whether or not he remembers who she is.
In the third part, a teenage girl travels from the future. She won't tell Nagare who she is there to meet. When Kei arrives, the girl asks Kazu to take a photo of the two of them together. Her camera is futuristic and as small as a credit card. Kohtake soon arrives and asks why Hirai's snack bar hasn't been open for two nights in a row. Kazu explains that Hirai's sister died in a road accident.
Hirai arrives dressed in mourning clothes. Her manner is brusque. She gulps down several glasses of water, then tells the others that neither parent spoke to her at the funeral. Hirai asks to travel back three days to the last time Kumi visited the cafe. To get the ghost to leave her seat, Kazu pours the woman refill after refill, having realized that the ghost always accepts more coffee. When the ghost goes to the toilet, Hirai takes her seat and Kazu pours her a cup.
Three days in the past, Hirai is kind and open with her sister. Kumi suspects something must be wrong, prompting Hirai's anxiety. Although she knows she can't save her sister, Hirai promises Kumi that she will return to Sendai and help run the family's inn. Kumi is delighted. Hirai learns that Kumi never resented her, as Hirai believed; instead, it was always Kumi's dream that they would run the inn together. Back in the present, Hirai resolves to fulfill her promise to her sister. Kei sees her out and rubs her pregnant stomach while smiling. Nagare looks at his wife and wonders whether she can give the child up.
In the fourth part, Kazu reads an email aloud from Hirai. Hirai says she is happy to be running the inn and mending her relationships with her parents. Fumiko is there, and she asks about time traveling to the future, which Kazu says is possible but would require the person you want to meet happening to be in the cafe at the same time.
Kei comes out of the back room looking pale. The narrator explains that Kei has always had a bad heart, and she was in and out of the hospital her entire life. It was while in hospital that she met Nagare, who'd been badly injured after being dragged by a truck. The narrator reveals that Kei is pregnant, and her doctor has warned that she will not survive giving birth. Nagare wants her to have an abortion rather than sacrifice her life, but he can't bring himself to tell her his opinion; it is up to her. Kei rests the rest of the day.
After the cafe closes that night, Kei comes out of the back room and tells Nagare she will go to the hospital tomorrow. Kei admits she is afraid that once she goes in, she'll never come out. Nagare realizes Kei is saying she will keep the baby, sacrificing her own life to have it. However, Kei is concerned about not being there to raise the child. She arranges to travel forward in time ten years; Kazu promises to arrange it so that the child will be waiting in the cafe. They decide on August 27—Kei's birthday—at three in the afternoon in ten years' time.
Kei arrives in the future to see that a man with a large scar on his forehead (Goro) is managing the place. Goro says that Nagare and Kazu are in Hokkaido. Kei assumes Kazu forgot her promise. However, the teenage girl who came to take her photo with Kei enters the cafe. She avoids Kei, but Kei notices she wears the wine-red apron that used to belong to Kei. When the phone rings, Goro brings it over to Kei. On the other end, Nagare says there was a mixup and Kei has actually traveled fifteen years into the future. The teenage girl is their daughter, Miki.
Fumiko arrives and gets the shy Miki to talk with her mother, saying that Miki has been looking forward to meeting Kei. Kei feels guilty for bringing the daughter fifteen years of unhappiness. However, Miki overcomes her shyness and thanks Kei for having given life to her. Kei returns to the present satisfied. She realizes that, for every time traveler, the benefit is that you can come back with a changed heart, even if you haven't influenced the course of events.
Kei checks into the hospital the next day and gives birth to a healthy baby girl the following spring. The novel ends in Kazu's thoughts as she considers how time travel at their cafe isn't quite as futile as people have called it. Kazu has witnessed many time travelers gaining strength in their hearts to overcome the difficulties they are facing. That is the chair's purpose.
