In School Days, the player assumes the role of Itou Makoto, a male high-school student who is considered attractive by his female classmates. One day Makoto notices a very beautiful girl at the school, and takes several pictures of her with his mobile phone. The girl who sits next to him in the class, Sekai, finds out about that, and helps Makoto to arrange a date with the mysterious beauty. But she cannot hide her own feelings for Makoto. As the story progresses, more characters become involved in the emotional drama, and Makoto will have to deal with some serious issues, depending on the choices he makes.

School Days plays similarly to other Japanese "digital novels" (such as Kana: Little Sister): the interaction is reduced to moments during which the player is able to choose an answer or an action for the protagonist of the game, influencing the progression of the story. However, "School Days" is more of an "interactive anime" than a novel. Instead of the traditional still images and text boxes the game has fully animated movie segments. The game contains explicit sexual scenes.

There are a total of 21 different endings, ranging from happy to very tragic.

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