In Iraq, a group of archaeologists discover ancient relics that prophecize the coming of a superior race and the end of all civilization. Meanwhile, back in Graviton City, as A-Ko and B-Ko's rivalry over Kei intensifies, Mr. Daitokuji sets up an arranged marriage between Miss Ayumi and Kei. Furious over the engagement, both A-Ko and B-Ko do whatever it takes to prevent the wedding from going through. Little do they know that another alien fleet is on its way towards Earth.

The CLAMP school, with its integrated curriculum from kindergarten to post-graduate studies, was founded by the largest of Japanese business empires, the House of Imonoyama. Funded entirely out of its own deep pockets, it was hoped that the school would be a haven for young men and women on whose shoulders our future would rest. The School is open to any talented individual, irrespective of his or her lineage or financial standing and is known to count scores of singularly talented pupils. It is furthermore also famous for its harboring of a remarkable percentage of party animals. Not even the bright and talented minds of CLAMP School can keep the campus free of crimes and mysteries. Or can they? Join Nokoru, Suoh and Akira, our case-cracking kid detectives, as they save the day and even the odd damsel in distress!

Yurume, an 18-year-old "ronin" and recent high school graduate, has high hopes of being accepted and attending Tokyo University. She moves into an apartment complex, the Maison du Wish, located on the outskirts of Tokyo where other ronins living there are studying for upcoming college acceptance exams.

Hidden away on a remote mountaintop, the Kokoro Library struggles to attract many visitors. Nevertheless, it is the home of sisters Iina, Aruto, and Kokoro, who consider it their mission to keep the library running in their parents' stead. Kokoro has long dreamed of becoming a librarian at the library with the same name as her, and tries her best to keep up with her older sisters. Due to the lack of patrons, the girls mainly spend their time sipping tea, chatting, and reading. However, as the number of mysterious visitors progressively increases, Kokoro begins to learn about the strange history of Kokoro Library—a place where small miracles seem to blossom.