The storyline of School Days revolves around Makoto Itou, who resides in the imaginary city of Haramihama with his divorced mother, who is heard but not seen. During his second term, Makoto begins to take an interest in Kotonoha Katsura, who happens to commute on the same train as him. Following a seating rearrangement in their homeroom, Makoto is introduced to Sekai Saionji, who later plays the role of a matchmaker for Makoto and Kotonoha. Sekai not only befriends the two but also provides them with a secluded spot to have lunch. However, Sekai starts developing feelings for Makoto herself and ends up kissing him at a train station.
As Makoto continues his relationship with Kotonoha and Sekai, he also becomes acquainted with other people, such as Setsuna Kiyoura, a shy member of the student council and Sekai’s lifelong friend, and Hikari and Nanami, friends of Setsuna and Sekai.
Makoto has two other friends who frequently appear in the story, namely Taisuke Sawanaga, his quirky best friend, and Otome Katou, a former classmate from middle school.
Since School Days takes place in the same universe, many characters from 0verflow’s previous visual novels either make an appearance or are mentioned.