Chronos, a shadowy group that opposes many politicians and commercial activity, reigns in the shadows. The plot begins when Train, also known as Black Cat, one of the organization's most formidable assassins, encounters Saya Minatsuki, a mysterious woman who always wears a bright kimono and softens her heart. As a result, he resolves never to follow instructions from anybody again or to murder for no cause. Saya is murdered by Creed, who refers to her as a witch, as well as Eve, the girl he cares for, a strange female with supernatural powers based on Nanotechnology and artificially developed by Dr. Tearju Lunatique. Later, Train discovers that Creed is establishing an association known as "The Apostles to the Stars," with the purpose of destroying the universe.