Near the end of the nineteenth century, as the balance of power shifts from Shogunate towards the emperor of Japan, Japan restlessly awaits the dawning of a new age. But not all are content.
Ryunosuke, a gifted swordsman plying his trade during the turbulent final days of Shogunate rule, has no moral code and kills without remorse. It’s a way of life that leads to madness.
Kenshin has settled into his new life with Kaoru and his other friends when he is approached with a request from the Meiji government. Makoto Shishio, a former assassin like Kenshin, was betrayed, set on fire and left for dead. He survived, and is now in Kyoto, plotting with his gathered warriors to overthrow the new government. Against Kaoru's wishes, Kenshin reluctantly agrees to go to Kyoto and help keep his country from falling back into civil war.
In 1879, Kenshin and his allies face their strongest enemy yet: his former brother-in-law Enishi Yukishiro and his minions, who've vowed their revenge.
When feudal lord Itakura Katsuakira decides to prepare his samurai troops for the onslaught of modernization by having them compete in a marathon, his independent-minded daughter Yuki secretly joins the race.
A sadistic Daimyo (feudal lord) rapes a woman and murders both her and her husband, but even when one of his own vassals commits suicide to bring attention to the crime, the matter is quickly hushed up. Not only will there be no punishment, but because the Daimyo is the Shogun's younger brother, he will soon be appointed to a high political position from which he could wreak even more havoc. Convinced that the fate of the Shogunate hangs in the balance, a plot is hatched to assassinate the Daimyo. The two most brilliant strategic minds of their generation find themselves pitted against each other; one is tasked to defend a man he despises, and has a small army at his disposal. The other is given a suicide mission, and has 12 brave men. They are the 13 Assassins.