Summer break has arrived, but while his other classmates are out having fun, Kimihiro Watanuki continues to work as compensation for the eccentric Yuuko in her shop. With the spirits and supernatural phenomena that bother him lessening, he pays his dues by cleaning, cooking, and doing whatever else the apparently lazy Yuuko needs. Watanuki, however, gets involved in a new predicament when Yuuko receives a mysterious invitation to a mansion whose owner seeks Yuuko's wish-granting ability. When he, Yuuko, and his classmate Shizuka Doumeki make their way to the peculiar residence, they meet others who were summoned by the same strange invitation. All of them are collectors of various unique items, drawn there by the chance to expand their collections. But as the collectors begin to disappear one by one, Watanuki and his companions must solve the mystery and put the case to rest, or find themselves in risk of danger.

Ten years after the events of xxxHOLiC Shunmuki, a melancholic Kimihiro Watanuki has taken over the shop formerly run by the mysterious Yuuko due to a promise he made to her. His companions Maru, Moro, and Mokona live together with him in relative contentment, and some familiar faces arrive every now and then: former rival turned-steadfast friend Shizuka Doumeki, and the former psychic prodigy Kohane Tsuyuri. While Kohane studies folklore under Doumeki at university, they encounter a case that is perfect for the master of the shop. Eventually, Watanuki receives a visit from Doumeki's grandfather, Haruka. He requests that Watanuki investigates his grandson's dreams. While inside the dream world, he discovers how their past adventures played out from Doumeki's perspective of view, leading Watanuki to discover truths from 10 years ago and secrets about the ties that bind their friendship.

Yuu Koito has always been entranced with romantic shoujo manga and the lyrics of love songs. She patiently waits for the wings of love to sprout and send her heart aflutter on the day that she finally receives a confession. Yet, when her classmate from junior high declares his love for her during their graduation, she feels unexpectedly hollow. The realization hits her: she understands romance as a concept, but she is incapable of experiencing the feeling first-hand. Now, having enrolled in high school, Yuu, disconcerted and dispirited, is still ruminating over how to respond to her suitor. There, she happens upon the seemingly flawless student council president, Touko Nanami, maturely rejecting a confession of her own. Stirred by Touko's elegant manner, Yuu approaches her for advice, only to be bewildered when the president confesses to her! Yuu quickly finds herself in the palm of Touko's hand, and unknowingly sets herself on a path to find the emotion which has long eluded her.