Though he grew up as an orphan, Nio Chirinu finds a place to belong: being a waiter at his adoptive grandmother's restaurant. But this peace does not last long; Nio and his sister Iroha are used as bait to arrest child abductors by Toshizou Hijikata and Souji Okita—two members of an infamous ronin group called Miburo. After the ordeal, Toshizou proposes that Nio join the ranks of Miburo and protect the people of Kyoto.

Frustrated by his own weakness, Nio trains to match the swordsmanship of his new comrades. Even so, he struggles to be accepted by Tarou Tanaka and Hajime Saitou, the other Miburo members of his age. Determined to befriend them, Nio must discover his own sense of justice and become strong enough to prevail against all his enemies.