The Melancholy of Haruhi Suzumiya follows the high school life of Haruhi Suzumiya, a young and very active high school girl, and those who are caught up in her antics. While Haruhi is the central character to the plot, the story is told from the point of view of Kyon, one of Haruhi's classmates.

Kyon is an ordinary freshman high school student who has recently given up his fantasies of espers, time travelers, and aliens as he left middle school. When he chooses to speak to Haruhi, he unwittingly sets off a chain of events which drag him into surreal situations; he is drawn further into a world eerily like the fantasies he had just managed to outgrow, with Haruhi at its center.

Searching for a group that interests her, Haruhi joins and quits every club in the school, finding only dissatisfaction. Kyon makes a snide remark about her actions and accidentally provides Haruhi the inspiration to create a club of her own. To help start the club, Haruhi forcefully drafts Kyon, who only stays in the club to protect other helpless victims of Haruhi's "voluntary arrests". As the story progresses, Kyon finds that each of these supposedly "helpless victims" has a specific reason to be there.