Tomoharu Natsume survived a horrible plane crash but Misao, his close friend, did not and became a ghost that continued to be attached to him. Three years later, he moved out to a place rented by his brother to live on his own and attend Raku High since his mother remarried. On his first day in his new house, a mysterious girl called Shuri turns up and gives him a silver briefcase to look after on behalf of his brother who lives abroad. Soon after, Tomoharu and his best friend, a ghost named Misao Minakami, are attacked by various factions who all seek the 'Asura Machina' and 'Extractor'.
