"Haganai: I Don't Have Many Friends" centers on Kodaka Hasegawa, a high school student who struggles to make friends due to his intimidating appearance and delinquent-like demeanor. After transferring to a new school, Kodaka finds himself isolated until he encounters Yozora Mikazuki, a loner who spends her time talking to an imaginary friend in an empty classroom. Recognizing their shared social struggles, Yozora proposes they form a club to help each other make friends. The Neighbors Club is established, with the goal of fostering social connections among its members.

The club attracts a diverse group of misfits, each with their own quirks and challenges. Sena Kashiwazaki, a popular and beautiful girl, joins the club despite her initial arrogance and disdain for others. Her rivalry with Yozora becomes a central dynamic, as the two frequently clash over their differing personalities and approaches to social interaction. Rika Shiguma, a science-obsessed classmate with a penchant for inappropriate humor, and Yukimura Kusunoki, a girl who believes herself to be a boy due to her upbringing, also become members. The group is rounded out by Kobato Hasegawa, Kodaka’s younger sister, who is obsessed with vampire lore and often refers to herself as a "true vampire."

As the Neighbors Club members engage in various activities, from playing games to hosting events, their interactions highlight their individual struggles with loneliness, self-identity, and societal expectations. Kodaka, as the de facto leader, often finds himself mediating conflicts, particularly between Yozora and Sena, while also grappling with his own feelings of inadequacy and confusion about his relationships. The series explores themes of friendship, belonging, and the complexities of human connection, often blending humor with moments of introspection.

The narrative progresses through episodic adventures and character-driven arcs, with each member of the club gradually opening up and forming bonds with the others. Despite their differences, the group’s shared experiences in the Neighbors Club provide a foundation for growth and mutual understanding. The series balances comedic elements with heartfelt moments, creating a story that resonates with themes of acceptance and the challenges of navigating social dynamics.