Kimihiro Watanuki's life was never really normal. But in addition to his ability to see spirits, this sequel to xxxHOLiC finds him still slaving away for Yuuko, the bizarre owner of a strange shop, who promised to rid him of this ability. However, this otherworldly woman can only do so when he has worked enough to earn his wish. Such is the way for anyone who finds their way into the shop to have their request granted: a compensation equal to their wish must be paid. In this odd shop that straddles the world of the living and the dead, Watanuki finds himself doing household chores for the seemingly lazy Yuuko and her companions, while also helping out clients. Along with his classmates, supposed romantic rival Shizuka Doumeki and his crush Himawari Kunogi, Watanuki deals with the many misfortunes surrounding Yuuko's customers, as well as those that closely follow him and his friends.

Kokone Morikawa has a strange napping disease that distracts her from reality, one that makes the world of her dreams and the real world near indistinguishable. In reality, she is an average high school student preparing for her university entrance exams; but in her dreams she is a magical princess of Heartland, a machine-driven future where the use of artificial intelligence is forbidden. Within the seemingly imaginary dreamland, Kokone discovers more about her family's past and the secret that her father, a talented mechanic, has tried to protect her from. However, as the events between two worlds intertwine, she must now protect the secret from villainous entities, both dream-like and terrifyingly real.

At the time of the ceremony of entry to the college, a young boy named Ushino Hayama finds Sara a girl whom he met ten years ago. From this day, a change has taken place in him, and notices that can now control some water. After having succeeded the swimming championships, he discovers deep sea diving.

Akihiro is a teenaged boy with fantasies. He's about to have date with his girlfriend Miyuki when he finds a strange carpet on his way home. Home, a pretty and over-energetic girl named Malon appears from the carpet. She tells Akihiro about the world of Phantasia and wants to live with Akihiro. But even if Akihiro loves pretty girls, he becomes angry with Malon's magical powers and drives her away. The maniac wizard, Roll, who wants to kill Malon, doesn't help at all.