"Genshiken" centers around the activities of a college club called the Society for the Study of Modern Visual Culture, or "Genshiken" for short. The club is dedicated to exploring and indulging in otaku culture, including anime, manga, video games, and cosplay. The narrative begins with Kanji Sasahara, a shy and introverted freshman, joining the club after struggling to find his place in college. Through Genshiken, Sasahara gradually embraces his otaku identity, forming friendships with fellow members who share similar interests.

The club is populated by a diverse group of characters, each with distinct personalities and levels of engagement with otaku culture. Makoto Kousaka, a skilled gamer and model student, is often seen as the club's de facto leader, though he is more reserved and less vocal about his hobbies. Harunobu Madarame, a loud and passionate otaku, serves as the club's most outspoken member, often engaging in debates and discussions about various aspects of fandom. Saki Kasukabe, a non-otaku who initially joins the club to spend time with Kousaka, provides an outsider's perspective, often clashing with the group's obsession with niche interests. Other members include Mitsunori Kugayama, a talented artist who creates doujinshi, and Ohno, a cosplayer who is deeply involved in the fandom scene.

As the series progresses, the club navigates the challenges of balancing their hobbies with academic responsibilities and social expectations. The narrative explores the dynamics of the group, highlighting their interactions, conflicts, and growth as individuals. The club participates in various activities, such as attending conventions, creating doujinshi, and organizing events, which serve as a backdrop for character development and exploration of otaku culture.

The story also delves into the relationships between the characters, particularly the evolving dynamic between Sasahara and Saki. Saki's initial disdain for otaku culture gradually softens as she becomes more involved with the club, leading to a deeper understanding and acceptance of her friends' passions. The series also introduces new members over time, such as Ogiue, a talented but socially awkward manga artist who struggles with her own insecurities and prejudices about otaku culture.

"Genshiken" is notable for its realistic portrayal of otaku life, avoiding exaggerated stereotypes in favor of a more grounded and relatable depiction. The series balances humor with moments of introspection, offering a nuanced look at the joys and challenges of being part of a subculture often misunderstood by mainstream society. Through its exploration of friendship, identity, and the pursuit of passion, "Genshiken" provides a thoughtful and engaging narrative that resonates with fans of anime and manga.