The story of Thirteen Assassins begins with a vassal of the Akashi caln committing seppuku in front of a daimyo's house. As it turns out, it's in protest to his lord raping and killing a girl and her samurai husband. This scandal is quickly covered up as the Akashi lord happens to be the Shogun's younger brother. What makes matters worse is that this reckless scoundrel will be soon appointed to a higher political position which could prove to be detrimental for the entire Shogunate. In response to that, a plot is hatched: 13 assassins will undertake the suicide mission to murder him on his way back from Edo.