Hourglass of Summer takes the player to a Japanese town where most of the young people go to school. The main character is no exception, he is waiting for the trimester and wants to immerse himself in the summer holidays, which begin in a day. The plot focuses on romantic relationships, telling how Kotaro Makimura fell in love with a girl from his school, Kaho Serizawa. She is popular at the school, and the guy does not dare to talk to her and try to gain her trust.

Returning home from school, the protagonist notices a strange girl following him, leaving a cloud of strange powder before disappearing. Confused, he reaches home and cannot understand what it was. The next day, he decides to try to understand what kind of girl he met. When he wakes up, he finds himself not on vacation, but at the beginning of September, when school starts again. He does not remember anything and does not understand how 3 months disappeared from his memory.

After talking to his friends and classmates, they pretended not to have seen him for three months, although no one considered it suspicious. He also learned that the girl he fell in love with died in a car accident in the summer. Unusual events will drag the young man through time between summer vacation, past and future. Finding himself in an unusual time jam, he meets that girl and gradually comes to her death, love and mixed feelings.