After the New Year, Yilin Jing comes to the Komatsu Detective Agency with a request. She wants to hire the trio as guides and bodyguards for the daughter of a Hong Kong tycoon who is visiting Kyoto in secret. Kiyotaka is forced to accept the request against his will, but luckily, Aoi comes to save the tour from becoming a total disaster. Everything seems to be going well at first, but before long, they find themselves caught up in an extraordinary incident!

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.

Aoi is in charge of Ensho’s upcoming exhibition at the Yagashira residence, but she is thrown for a loop when he suddenly refuses to hold it, making her scramble to change his mind. Meanwhile, Atsuko, who runs an underground club in Gion, comes to Kiyotaka with a strange request. The Komatsu Detective Agency begins to investigate, but things take an unexpected turn as the full story gradually comes to light...

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!

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...

Aoi has graduated from high school and successfully enrolled in her top pick, Kyoto Prefectural University. Kiyotaka has completed grad school too, and their relationship can finally deepen—or so they thought, but the owner orders Kiyotaka to learn more about the world by working outside of Kyoto! His first placement is at Shokado Garden Art Museum in Yawata City. One weekend, Aoi and Kaori secretly pay his workplace a visit to see how he’s faring, but as it turns out, an unexpected incident is awaiting them there!