Shinomori Aoshi was raised a ninja of the Oniwabanshū, who worked for the Shogunate government during the Edo period. He helped to raise Makimachi Misao from childhood as a member of the Oniwabanshū.

After the revolution, since a few members of the Oniwabanshū were unable to adapt to life in the Meiji era, Aoshi and these members worked for the corrupt, power-hungry business man, Takeda Kanryū instead. Aoshi's subordinates included Beshimi, who specialized in darts and poison; Hyotoko, whose name literally means "Fire Man" and uses flint-and-steel teeth to breathe fire; Han'nya, a skilled martial artist, deft ninjutsu practitioner and Aoshi's student; and Shikijou, a "muscle man."

Aoshi himself remains an enigma. He rarely (if ever) shows emotions in or out of a battle. His weapon in the beginning of the series involved only one kodachi (in combination with martial arts). However, after his defeat at Himura Kenshin's hands at Kanryu's mansion, he dedicated himself fully to revenge for the sake of his fallen comrades. When Aoshi next appears, he uses double-kodachi, and seems to have fully disregarded his emotions in order to kill Himura.

They fight at Shishio Makoto's mansion in order to settle the score, and upon the battle's break, Aoshi realizes where he went wrong, and becomes somewhat of an ally.