Rurouni Kenshin: New Kyoto Arc: Cage of Flames.

Although she's only sixteen and looks even younger, Misao Makimachi is already a skilled and competent member of the Oniwabanshu ninja clan. That's fortunate for Misao, because her onimitsu talents may be all that keeps her alive when a journey in search of the leader of the clan, Aoshi Shinomori, leads her instead into a face-to-face encounter with an even more dangerous man and a plot to overthrow the Meiji government! Quickly enmeshed in the affairs of the legendary assassin Hitokiri Battosai, now known as Kenshin Himura, wielder of the reverse-blade sword, Misao finds herself pulled into the middle of a deadly intrigue against Makoto Shishio, who is orchestrating the conquest of all Japan - beginning with Kyoto!