The story of Hantsuki focuses on the budding relationship between the seventeen years old Yuuichi Ezaki and Rika Akiba. Both are hospitalized in Yuuichi's home town for their respective conditions. Yuuichi 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.