Sasahara Kanji is a college freshman who decides to join a student society to share his hidden thoughts on manga, anime and gaming. When he first visited Genshiken, short for "Gendai Shikaku Bunka Kenkyuu Kai" (Society for the Study of Modern Visual Culture), his groundless pride was destroyed by the plotting of Madarame, a sophomore student in Genshiken, but he still couldn't admit that he is an otaku. However, as he participates in society activities such as visiting dojin (private publishing) shops and anime festivals, and hangs out with other society members Kosaka (a hardcore otaku despite his extreme eccentricities and good looks), Kosaka's girlfriend Kasukabe Saki (who isn't really an otaku), Ohno (a cosplayer) and the others, he opens his mind and resolves that he will make his way into the otaku world. With their help, Sasahara slowly adjusts to otaku life in Genshiken.

The Society for the Study of Modern Visual Culture, otherwise known as Genshiken, is now under the charge of a more confident Sasahara. Things have changed in between semesters, and the otaku club now has a new otaku-hating member named Ogiue. Sasahara's initial goal of starting a doujin circle and selling those fan-made magazines at the next Comic Festival becomes a reality, but reality is a cruel master... who apparently crossplays. Afterward, the club is abuzz with talk about Tanaka and Ohno's relationship, which takes a hesitant step forward.

Another college semester begins and the returning members of Genshiken attempt to recruit new club members. Three new members join the club, attracted by Ogiue's BL drawings. She welcomes the new members but fears the club will become a "rotten girls" haven for yaoi fans and is getting a bit too far removed from it's original purpose.