A bullied teenage boy wakes up in the future after going into cold sleep. His new high school is filled with nothing but girls, and more than a few of them seem to have an interest in him, especially his old teacher.
Reito goes to visit the widow of the very first victim of the MK Virus in Japan. The widow knows more than she should, and is secrelty in contact with someone very important to him.
Reito finds clues leading to the origin of the MK virus. He also finds out that anybody who researches the origins of the virus tends to go missing quickly.
As Shouta becomes accustomed to life as the only boy at school, he starts to seek out more and darker thrills. And his keepers are more than happy to oblige his every need.
The Numbers come under attack from terrorists calling themselves Izanami. But one of Izanami's leaders is the girl Reito's been searching for since he woke up.