The story revolves around a love triangle between the male protagonist, Makoto, and two girls in his year, Kotonoha and Sekai.

Makoto develops an interest in Kotonoha, and although they both take the same train to school, she seems to be unaware of his existence. One of his classmates, Sekai, gets the two together despite holding strong feelings towards Makoto.

Yuuki Ashikaga is a high-school freshman at Sakakino Academy. While working as a student librarian, he grows enamored of Kotonoha Katsura, a girl who frequents the library. Unfortunately, Kotonoha is already dating Makoto Itou, another schoolmate.

The situation is further complicated when Chie, Yuuki's older sister introduces him to Roka Kitsuregawa, her kouhai in the basketball club. Roka becomes interested in Yuuki, who only has eyes for Kotonoha. In order to make him jealous, Roka lies and claims she already has a boyfriend, her former classmate Makoto Itou. Unfortunately for all of them, Roka's lie sets off a chain of events no one could have predicted...

Note: Cross Days takes place in the middle of the original School Days storyline and provides an alternate take on how things might have turned out.