The story of Hantsuki focuses on the budding relationship between the seventeen years old Yūichi Ezaki and Rika Akiba. Both are hospitalized in Yūichi's home town for their respective conditions. Yūichi has hepatitis A, while Rika has problems with a weak heart valve. These teens would then fall in love while they spend time with one another. The story is based in Ise, Mie prefecture as implied by the "Welcome to Ise" sign shown after the opening sequence in the first episode of the anime series.

During the winter, Yuichi was hospitalized due to hepatitis. Randomly he would try to escape from the hospital but would get beat up by the nurse. One day, he happened to meet Rika, a girl of his age, in the next building. He was fascinated by her beauty, but she was very selfish girl. Although she led him by the nose, he began to be attracted by her. However, when Rika told him about her illness, he knew why she acted so selfish; she didn't have long to live.

In a world where everything was lost, our paths crossed. An unidentified epidemic exterminated humans in half a year. Hazufumi, a teenager who miraculously survived, lived lonely in this desolate world. He rejected to attain important things because he knew the pain when losing them... He happened to cross by a girl. A weird girl being followed by a hundred cats.And meeting with her changed Hazufumi's heart. (Source: Baka-Tsuki)