Tomoya Okazaki is a third year high school student whose mother died when he was young, leaving his father to raise him. Severe drinking problems caused Tomoya's father to become violent; during one of the quarrels, he injured his son. Their relationship has seemingly improved since then, but Tomoya's injuries, mental and physical, have led him to a delinquent life. This changes when he meets Nagisa Furukawa, a soft-spoken girl who gets sick easily. Tomoya begins to help her reform a drama club she failed to join last year, and gradually changes his view about life.

Clannad is a visual novel. The game is dedicated to the development of the story, displayed as still images accompanied by text. The player's interaction is confined to occasional "decision points", which prompt him to make choices for Tomoya, altering subsequent events. The game is divided into two parts; the second one describes the lives of its main characters some time after the conclusion of the first one. In order to access the second part, the player has to play through all the scenarios of the first one, which are only possible to achieve by replaying it and making different choices each time.

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