Half a year after moving to Kyoto, high school girl Aoi Mashiro brings her late grandfather’s old scrolls to Kura, an antique store nestled in Kyoto’s Teramachi-Sanjo shopping arcade, for an appraisal. One thing leads to another, and she winds up working there part-time. The manager’s son, Kiyotaka Yagashira—nicknamed the “Holmes of Kyoto”—is uncannily perceptive, and together, they solve strange cases relating to the antiques brought to them by clients.

Kiyotaka and Aoi have finally confessed their feelings for each other and are now dating. One day, they learn of a string of thefts in Kyoto: someone is stealing Buddhist works of art from art collectors. Then Komatsu, the detective they met at Yoshida-Sanso Inn, comes to Kura to ask for help finding his missing daughter. The two cases turn out to be intertwined...

Kyoto bustles with the arrival of the New Year and Aoi Mashiro continues to work at the antique store Kura in the Teramachi-Sanjo shopping district, alongside the owner’s grandson, Kiyotaka Yagashira. On Valentine’s Day, the two of them are invited to a storytelling session at the Yoshida-Sanso Inn, hosted by the popular mystery author Kurisu Aigasa. There they find out that someone tried to murder her three months ago, and her sister asks Kiyotaka to find the culprit.

It’s November and winter is just around the corner. Aoi Mashiro continues to work at the antique store Kura in Kyoto’s Teramachi-Sanjo shopping district, alongside the owner’s grandson, Kiyotaka Yagashira. Nicknamed “Holmes,” he’s a young Kyoto man with a bit of a wicked streak. One day they’re visited by a famous kabuki actor named Kisuke Ichikata. Minamiza Theatre’s annual grand show is coming up in December and Kisuke has received a threatening letter. The next day, Kiyotaka and Aoi go to watch him on stage, where he suffers a serious injury. Unrequited love, illicit affairs, hidden feelings—the mysteries continue through Christmas and New Year’s in Volume 3 of Holmes of Kyoto!

It’s the winter of Aoi’s second year in university, and she’s been tasked with planning an exhibition of Ensho’s paintings at the Yagashira residence. As she’s struggling to come up with ideas, she joins a student group aimed at bettering the city of Kyoto, and the Kita-ku ward office asks for their help in revitalizing the Mount Funaoka area. Meanwhile, Kiyotaka receives an unusual request from Atsuko, who runs a flower arranging school and an underground club in Gion, and wants him to investigate her student’s fiancé on suspicion of cheating.

High school girl Aoi Mashiro has begun her part-time job at the antique store Kura in Kyoto’s Teramachi-Sanjo shopping district. There, she works with the store owner’s grandson, Kiyotaka Yagashira. Kiyotaka is a young Kyoto man with a gentle demeanor—as well as a fearsome intuition and a bit of a wicked streak. One day, a first-time visitor brings a tea bowl for Kiyotaka to appraise. Kiyotaka immediately identifies it as a fake. Then he and Aoi encounter a priest who introduces himself as Ensho. This man turns out to be an extraordinary counterfeiter. The mysteries continue in Volume 2 of Holmes in Kyoto!

Aoi is now in her third year of high school, with entrance exams looming on the horizon. She and Kiyotaka are slowly and clumsily growing closer, but one day, Ensho—Kiyotaka’s nemesis—shows up and asks him to appraise a white porcelain incense holder. However, when Kiyotaka claims that it’s real, the counterfeiter denies it and leaves in an attempt to discredit him. Some time later, Aoi is approached by Ensho after school. Kiyotaka arrives just in time to save her, but then he breaks up with her, sending her into the depths of despair. Two months later, Aoi receives a phone call from the manager. “Kiyotaka came back from Hyogo,” he says. What will become of the two now?