After the bloody battle against Hades, the goddess Athena and her saints are still recovering when they find themselves face to face with their newest and most formidable foe: the dreadful moon goddess Artemis. Artemis replaces Athena as the earth guardian deity and takes over the Sanctuary, turning Athena's Saints into her servants. Upon invading the Sanctuary, the Bronze Saints learn that Athena was banished by Artemis and decide to fight the moon goddess in order to rescue their true goddess and free the Earth from Artemis's ominous control.
Demons that once almost destroyed the world, are revived by someone. To prevent the world from being destroyed, the demon has to be sealed and the only one who can do it is the shrine maiden Shion from the country of demons, who has two powers; one is sealing demons and the other is predicting the deaths of humans.
A 14th century Crusader returns with his comrade to a homeland devastated by the Black Plague. The Church commands the two knights to transport a witch to a remote abbey, where monks will perform a ritual in hopes of ending the pestilence.
In February 1999, a string of murders has Shiki Ryougi and Mikiya Kokutou on edge. These crimes share a disturbing resemblance to a similar set of homicides from 1995, when Shiki and Mikiya first met, and awaken a dark, murderous desire that has laid dormant within Shiki's soul ever since then.
August 1995: Mikiya first meets Shiki in a white kimono during a snowing day. Later on, at the high school freshmen ceremony, Mikiya sees Shiki in the crowd and chases after her, introducing himself to her.
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.
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.
On a future Earth, war between the Kingdom of Honneamise and its rival, The Republic, is inevitable. As evolving technology creates new ways to wage war, a small group seeks to propel mankind into space in their world’s first spaceflight program.
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.
Two FBI agent brothers, Marcus and Kevin Copeland, accidentally foil a drug bust. To avoid being fired they accept a mission escorting a pair of socialites to the Hamptons--but when the girls are disfigured in a car accident, they refuse to go.
In order to murder Tokugawa Ieyasu to overthrow his reign, Sarutobi Sasuke put a group of young men under a cruel and deadly form of trainment to become ninjas.