Yuuki Ashikaga is a high-school freshman in his second semester at Sakakino Academy, who from his regular visits to the school library, grows enamored by Kotonoha Katsura, a fellow classman who comes by to read. Despite already having a boyfriend, she genuinely reciprocates his interest. However things get complicated when, following a brief encounter, his sister, Chie Ashikaga, introduces him to Roka Kitsuregawa, an acquaintance who also becomes infatuated with him. Out of jealous spite for her rival, Roka attempts to dissuade Yuuki by claiming to like Makoto Itou, another schoolmate. Her lie dramatically backfires, as Yuuki, aware that Makoto is Kotonoha's boyfriend, goes to ask her about the affair.

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.