In an alternate version of the present, Tokyo has been decimated by a shocking terrorist attack, and the only hint to the identity of the culprit is a bizarre video uploaded to the internet. The police, baffled by this cryptic clue, are powerless to stop the paranoia spreading across the population. While the world searches for a criminal mastermind to blame for this tragedy, two mysterious children - children who shouldn't even exist - masterfully carry out their heinous plan. Cursed to walk through this world with the names Nine and Twelve, the two combine to form "Sphinx," a clandestine entity determine to wake the people from their slumber - and pull the trigger on this world.

Ten years have passed since the end of Bakumatsu, an era of war that saw the uprising of citizens against the Tokugawa shogunate. The revolutionaries wanted to create a time of peace, and a thriving country free from oppression. The new age of Meiji has come, but peace has not yet been achieved. Swords are banned but people are still murdered in the streets. Orphans of war veterans are left with nowhere to go, while the government seems content to just line their pockets with money.