The narrative of Hana no Miyako revolves around Miyako Arima, cousin of Shiki Toono in a universe separate from Tsukihime and Melty Blood.
Shiki Nanaya finds himself in a bit of a pickle as he is the weakest member of the Aikido club and is responsible for recruiting a new member. He believes Miyako Arima would be ideal for the role, but she appears disinterested. To make matters worse, strange individuals target her at school, making her existence even more complicated. What choices does she have?