Sorry for the large file size! >_< There was a lot of story to cover in the game!
The Melancholy of Haruhi Suzumiya follows the high school life of Haruhi Suzumiya 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 a first year in high school who has just recently been able to leave his fantasies of espers, time travelers, and aliens behind him along with middle school. However, when he chooses to speak to one eccentric girl by the name of Haruhi Suzumiya on the first day of high school, he unwittingly sets off a chain of events which drags him into situations entirely different from the real world in which he had convinced himself he was a part of. This turns his world nearly upside down as he is drawn further into a world eerily like the fantasies he had just managed to outgrow, with Haruhi Suzumiya at the center of it all.
Searching for a group that interests her, Haruhi joins and quits every club in 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 (or try to protect) other helpless victims of Haruhi's "voluntary arrests". However, as the story progresses it is revealed that each of these supposedly "helpless victims" has a specific reason to be there.
Except for Kyon, all the students in the club are secret agents of various organizations who are sent to observe Haruhi. They gradually explain that Haruhi has superhuman control over every aspect of the universe - an ability she is unaware of. Whenever Haruhi becomes bored or otherwise dissatisfied with reality, she unconsciously creates a new universe - one more to her liking - and attempts to switch over. This leads to the destruction of the current universe. To prevent this, the members of Haruhi's club spend most of their time trying to keep their god-like leader entertained, hold her powers in check, and maintain the illusion that she is living a normal life.