The story starts following an incident: a young girl jumps from the top of a building. The image provokes a certain dread, as the girl appears to have been a corpse even before she jumped. The case is dismissed, yet more and more of these suicides occur, and all from the same building. Thus began the rumour, that a ghost inhabited the rooftop of the building.

July 1998 - After a group of delinquents is found dead in their hangout place with all their limbs twisted and torn off, Aozaki Touko receives a request to find the murderer and asks Shiki for help. The main suspect is Asagami Fujino; a girl who was the boys' plaything until recently, who Shiki believes to be "one of her kind".

Tomoe Enjou is attacked by bullies from his old school and saved by Shiki Ryougi. He asks her to hide him at her place and admits that he killed someone. Several days later, there are still no broadcasts about the murder as if it didn't happen... and when the victims are found, they're alive and unharmed.

January 1999: Apprentice mage Azaka Kokutou, Mikiya's younger sister, has been ordered by her mentor, Touko Aozaki, to investigate a certain incident in which fairies steal the memories of students at Azaka's school, Reien Academy. Azaka launches an investigation with the help of Shiki.

In the year 2220 A.D., the Earth Federation launches a plan to evacuate Earth when discovering that a travelling black hole capable of destroying anything in its path is on course towards the solar system. As the people on Earth prepare to relocate to planet Amare, whose ruler offers refuge, the tyrants known as the "S.U.S. Empire" attack the first Earth evacuation fleet. After learning that his wife Capt. Yuki Mori-Kodai disappeared in the battle and that legendary space battleship Yamato has been fully rebuilt, Susumu Kodai accepts command of the ship as he intends to not only help humanity once again, but also find Yuki in the hope of helping his relationship with his daughter Miyuki, who puts the blame on him for her mother's disappearance. But in order to fullfil the mission, the Yamato must go through battles against the SUS Empire, who intend to spoil humanity's hopes of finding a new place to live in and turn Earth into energy for their own selfish needs.

In Enchanted Parade, Akko, Lotte and Sucy, having gotten in trouble yet again, are forced to team up with three other troublemakers; Amanda O'Neill, Constance Braunschweig Albrechtsburger and Jasmineka Antonenko, and must make an annual witch parade a success or else face expulsion.

Tobias, Mary, and Sakuya are way into the The World. Together, they form an inseparable group, grinding toward the break of day and running dungeons in search of the artifacts of adventure. But when the trio becomes lost in this virtual labyrinth, a chance encounter with the mysterious entity known only as Hermit will change their lives forever.

There is a small town on the sea. Raika just enjoys his school life with Ibuki, his old friend, and Yuri, his maid. However, his father is actually a magical girl (?). Also, a group of magical girls come to his school to look for a treasure stone called Mana Prism. Though he doesn't want to wear a girl's costume, he is forced to be a magical girl as well! "Come back, my peaceful life!" To save his school, his battle against the magical girls starts now!

Noel is an 11-year-old girl who despises Christmas. She has lived with her father ever since her parents divorced three years ago, but her father ends up busy at work every Christmas and she cannot play with her friends from school. On a lonely Christmas Eve, Noel takes her usual apartment complex elevator ride to her home, but when the doors open, she finds herself lost in a humongous factory—owned by Santa Claus. Santa Claus has gone corporate as Santa Company with the motto "Swiftly, surely, secretly." The outfit takes orders and delivers top-notch presents to children in the utmost secrecy. Noel meets some new friends, and together, they take off in a sled to deliver presents.

In 202X, Tathagata Killer, a mysterious military leader armed with extraterrestrial technology, stages a coup and becomes the new emperor of the world superpower of Asia. Sho Shishimaru, gifted with prophetic powers, may be the only one standing in the way of Killer’s take-over of the entire world. The future of humankind is at stake in this epic struggle, but in its midst, we learn about the mystical laws that rule the world around us.