Two years have passed since the final battle with Sephiroth. Though Midgar, city of mako, city of prosperity, has been reduced to ruins, its people slowly but steadily walk the road to reconstruction. However, a mysterious illness called Geostigma torments them. With no cure in sight, it brings death to the afflicted, one after another, robbing the people of their fledgling hope.

Izo, a Ronin, and Raiden, an orc, work to bring a young elf girl and the wand she carries to the land of the elves in the north.

Under constant attack by monstrous creatures called Angels that seek to eradicate humankind, U.N. Special Agency NERV introduces two new EVA pilots to help defend the city of Tokyo-3: the mysterious Makinami Mari Illustrous and the intense Asuka Langley Shikinami. Meanwhile, Gendo Ikari and SEELE proceed with a secret project that involves both Rei and Shinji.

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.

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. But Shiki hides a big secret: A wave of bizarre murders occur around many loose ends, and no suspects. there are still many questions: Who to believe? Who is the murderer? What is the secret of Shiki? and especially: Who is SHIKI?

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".

June 1998: After spending two years in a coma caused by a traffic accident, Shiki Ryougi awakens with amnesia. She is visited by Touko Aozaki, a wizard and proprietor of a studio called Garan no Dou. Shiki has lost not only the memory of her accident, but also any real sense that she's even alive. Strangely, enigmatic beings begin to attack 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. 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 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.