Yuichi hasn’t seen his cousin Nayuki in years. Now that he’s back, all knowledge of ever visiting has vanished. He tries to adjust to the vaguely familiar surroundings, but the gaps in his memory haunt him as time grows short. The pieces of the puzzle have appeared – an eerily silent beauty with blazing tresses, the mysterious girl with the winged backpack, and the sword-wielding demon slayer – but it’s up to Yuichi to discover how they fit together.

Mikan Sakura is a normal 10-year-old girl. Optimistic, energetic, and overall a very sweet child, Mikan is the complete opposite of the aloof, intelligent, and somewhat cold-hearted, Hotaru Imai. Despite their glaring differences, the two girls have been best friends for a very long time. So when Hotaru suddenly transfers to Alice Academy, a prestigious school in the city, her best friend is devastated—especially when she hears of the horrible rumors regarding the academy's harsh treatment of students. Beset with worry, Mikan runs away to see her best friend!

Saotome Kazuya is threatened with a computer virus. Trying to stop the virus, he makes a special order. May is a cyberdoll that arrives at his door a few minutes later and she is 1/6th the size of a normal person.

The Mobile Shinsengumi was organized for the specific reason of keeping Kyouto safe from influences which would hinder Japan's efforts towards westernization, be those demons and monsters of every shape and size or a band of misanthropes bent on turning the clock back for the city of Kyou. Yuuko Kondou, Toshie Hijikata, and Kaoru Okita are daughters of the reknowned Isamu Kondou, Toshizou Hijikata, and Soushi Okita, leaders of the feared, original Shinsengumi. They have come together under the banner of "Truth" as their fathers once had and under the guidance of Ms. Oryou. With the help of Oryou's son Ryuunosuke, Shintarou, Gennai, and the cat monster Nekomaru, they protect Kyouto from the evil that lurks in the shadows. But, who protects the people of Kyouto from the Mobile Shinsegumi?