Genshiken takes Sasahara to Akihabara for dōjinshi shopping while Kohsaka and Kasukabe go to Harajuku for clothes; Kasukabe discovers Kohsaka's hentai collection and gets an introduction on the subject from the others.

Genshiken goes on a club trip to Comifes, a large comic convention; Madarame seriously injures his hand, but pretends to be fine in the name of fandom until the pain becomes too great to bear.

Ohno is introduced as she joins Genshiken, while Genshiken takes part in a university club fair and Kasukabe's ex-boyfriend pays her a visit.

Due to Genshiken's lack of "activities" as defined by the school, the club is threatened with closure; salvation comes from an unlikely source as Kasukabe intervenes personally.

Kasukabe tries to make herself more appealing to Kohsaka by taking an interest in his hobbies by trying to learn how to play Puyo Pop Fever. Sasahara's sister Keiko also makes an appearance and calls on her brother for help.

Two freshmen take an interest in Genshiken and join them for a night out on the town. Kasukabe, however, has no intention of making them feel welcome.

Ohno and Sasahara start a plamo project and get the whole club involved, while Kasukabe learns an important lesson.

Madarame is stuck in the club room with Kasukabe and tries to strike up a conversation, running through different scenarios in his head which parody the visual novel format.

The club, along with Keiko, pays a visit to the beach, much to the dismay of some of the members; Keiko decides to compete for Kohsaka's feelings and tries to become an otaku.

Kasukabe decides the club room needs a cleanup, but an accident causes Genshiken to be banned from the university fair. As an apology, Kasukabe takes Ohno's place in the fair's cosplay contest.

The club is depressed due to their punishment of community service. Sasahara becomes the new President and proposes that the society attend Comifes as a circle.

hings are looking up for Sasahara as the Genshiken secures a spot among the dōjinshi vendors at the next Comifes, but the devil is in the details as they quickly need to figure out the finer points of actually making one. An unexpected relief comes when Ogiue actually volunteers her services (if in limited quantities), but will the new President have what it takes to stand up to the other obstacles in their way?

It's nearing the end of July, and with the deadline for finishing their dōjinshi looming, all the club has to show are the two pages drawn by Ogiue. With Kugayama's continued lack of material pushing the deadline (and Sasahara's patience) to the limit, it looks like they'll have to put aside their differences (and their sleep cycles) to get things done on time.

The day of Genshiken's participation in Comifes has arrived, and they are finally set to take their place as a vendor. But despite (or because of) Haraguchi's "blessing," sales are initially slow. Ohno's arrival (in cosplay, naturally) seems to change their luck for the better, but things really get underway with a surprise appearance. How Kasukabe will react to it, however, is another matter entirely.

Ohno likes Tanaka, Tanaka likes Ohno. Both however are too shy and lacking confidence to make a first move. With the rest of Genshiken in a state of concern and confusion over their relationship, Ohno confides in Kasukabe her anxieties and Kasukabe suggests a possible approach that may give both of them the courage to confide their affections.

Ogiue catches Sasahara and Madarame in an unintentionally-compromising position, setting her fujoshi imagination alight with various slash pairings between her fellow club members. She may have just found the inspiration to make a dōjinshi for next summer's Comifes, but her sketch of Sasahara gives Saki other ideas.

Genshiken is making preparations to go to the upcoming Winter Comifes as a group, but when the other members invite Ogiue along, she adamantly refuses. That doesn't stop her from appearing anyway in the guise of her high school persona to buy all the latest yaoi dōjinshi, but things get complicated as she (literally) runs into the rest of the club.

Graduation time is finally upon Tanaka, Kugayama, and Madarame, and with it come emotional reflections on the past three years for the club. The presidential torch is passed on, and a Kujibiki Unbalance OVA finally gives closure to the first season, but what about Madarame's job hunt? And for that matter, what will become of the Genshiken under President Ohno?

It's the beginning of the school year, and Ohno is planning out her first year as the president of the Genshiken. How will the club change under her cosplay management? Also, Ogiue learns that she's accepted to Comifes and tries to work up the courage needed for her debut. But will the newest iteration of the club sink or swim, and will Kuchiki be Ohno's nemesis, or her unlikely savior?

Sasahara's job search is not going as well as he'd hoped; at every turn, his negative portrayal of himself and uncertainty over his own beliefs make companies balk at hiring him. Meanwhile, Kousaka's absence is starting to get to Saki, while Ogiue struggles to draft her Comifes dōjinshi without any interference from Ohno's fetishes. But could Kuchiki be on to something about Sasahara and Ogiue?

As Ogiue continues her preparations for Comifes, now a few days away, friends of Ohno's from the US show up unexpectedly to come to convention as well. While the foreign otaku ways of Angela and Sue shake up the (somewhat) peaceful clubroom, perhaps Angela is the "sensible" one when it comes to understanding the feelings of others.

As Comifes starts, Sasahara help Ogiue set up her doujinshi booth. Angela cosplays with Ohno in the costumes Tanaka made for them, while Sue wonders around the convention. Sue eventually obtains one of Ogiue's doujinshi books, and ask her to sign it, claiming it is "real hardcore." At a bathhouse, Ohno wonders why her plan to make Sasahara and Oguie a couple is failing. After Comifes is over, Sue and Angela leave to go back to the United States, with Ohno shipping the massive amounts of doujinshi to them later.

Failing continually at his job interviews, Sasahara begins to lose sight of what he's working towards. He finds himself settling to apply for any available opening, and ends up on the brink of giving up altogether. It takes some harsh words and tough love from the rest of Genshiken to convince him to try one more time. And for that matter, how are the other members making out?

With Ogiue as new president and several of the original members already graduated, four new members join the society: Ohno's friend Susanna, the loud Rika Yoshitake, the grumpy Mirei Yajima and the mysterious Hato Kenjirou. The new members join the club attracted by Ogiue's yaoi drawings. She welcomes the new members but fears the club will become a "rotten girl" (fujoshi) haven for yaoi fans and that is getting a bit too far removed from its original purpose.

Hato has a difficult time with Yajima and Yoshitake's obsession over his crossdressing. Keiko Sasahara, Kanji's kogal sister, appears in the club's room while Madarame is in there thinking about Saki Kasukabe. Ogiue recruits Genshiken members as employees to help in her manga artist work.

After Madarame lends a thankful Hato his place to change into girl's clothes, both start to become good friends. The group continues their work helping Ogiue finish the club's doujinshi for the Summer Comifes.

Angela returns to Japan to visit the Summer Comifes and do some cosplay with Ohno like she does every year. Two girls from Ogiue's past make an unexpected visit to the club's booth, much to Susanna's chagrin.

In the final day of the Summer Comifes, Angela's sudden and vocal interest in Madarame make him and the rest of the Genshiken have an utterly embarrassing moment. However, Hato's timely confession to the group may be even more shocking than that.

The group has to deal with the aftermath of Hato's confession and its embarrassing (but hilarious) effects on Madarame, Kuchiki and the rest of the Genshiken. A relative of Yoshitake visits the club's room to know more about the University and the otaku society.

Ogiue plans to make a romance manga story for the club's magazine that is going to be published at the Campus Festival, so she asks the members of Genshiken about their past relationships during High School for inspiration. Hato reveals the full extent of his artistic skills and the strange condition that limits them.

Hato talks with Madarame at his apartment to apologize for his actions during the last Comifes. The members of the otaku society struggle to complete their manga stories for the club's magazine.

The Genshiken members successfully participate in the Campus Festival activities, but several different persons from Hato's High School days make an unexpected appearance at the University.

Hato comes to terms with his past and finally reveals the true reasons for his crossdressing. Saki Kasukabe arrives at the Campus Festival just in time to discover Madarame and Susanna in a compromising position.

In the epilogue of Hato's revelation another situation ensues. Madarame and Saki are tricked to be reunited alone in the club's room by Sasahara and a dubious Hato.

After a long and emotional struggle Madarame finally has confessed his feelings to Saki (sort of). Both new and old members of the Genshiken support their fellow otaku friend in the only way they know. Ohno's angst about her future with Tanaka and life after graduation make her cosplay to an extreme.

The Genshiken club members travel together to a spa resort. By using her own personal experiences as an example, president Ogiue gives a troubled Hato some important lessons about love, friendship and mutual understanding.