Kasumi Kogen, which translates to "The Village of Mist", is a town somewhere in rural Japan. In this town there is a school, the Shinobi Gakuen, where competent female students gather from all over Japan and train to become kunoichi (female ninja). The people of Kasumi Kogen are alumni of the school, and they run and jump and disappear as if the whole town were a big ninja house.
The story begins as a girl, Himawari Hinata, arrives in Kasumi Kogen. She has transferred to Shinobi Gakuen to train under Ichikawa Raiso and fulfill a dream of becoming a kunoichi that she has fostered since she was saved by one in her childhood. On her first day, she meets Hayato Marikoji, a teacher who is himself just arriving at Shinobi Gakuen, and he saves her life. Hayato does not possess any ninja skills; he is teaching the students about normal Japanese society in order to pay a large debt. However, Himawari notices that Hayato bears the same mark on his neck as the ninja who saved her when she was young.
Himawari! is the story of Himawari and her journey to become a kunoichi, and the vow she makes to protect her sensei.