| ShortSummary | - 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.
- 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 to the limit, it looks like they'll have to put aside their differences to get things done on time.
- 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 runs into the rest of the club.
- 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 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 her anxieties to Kasukabe, who suggests a possible approach that may give both of them the courage to confide their affections.
- Ohno and Sasahara start a plamo project and get the whole club involved, while Kasukabe learns an important lesson.
- The day of Genshiken's participation in Comifes has arrived, and they are finally set to take their place as a vendor. But despite Haraguchi's "blessing," sales are initially slow. Ohno's arrival 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.
- 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 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 wanders 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.
- An introduction episode explaining how Kohsaka, Kasukabe and Sasahara got involved with Genshiken; after some uncertainty, Sasahara decides to fully participate in the club.
- 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.
- Two new members join the society: the abrasive Manabu Kuchiki and the standoffish Chika Ogiue. Ohno hatches a plan to trick Ogiue into revealing her true inner self.
- 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?
- Things 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 , but will the new President have what it takes to stand up to the other obstacles in their way?
- 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.
- 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.
- 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.
- 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?
- 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.
- At Kasukabe's urging, Madarame sets out in search of a less otaku-ish outfit. Later, a heart-to-heart over sushi reveals that they might not be from completely different worlds after all. Unfortunately, this only confuses him more.
- 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.
- 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?
- 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.
- 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?
- 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.
- 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.
- The school festival approaches, and Ohno is committed to another cosplay photo shoot. But tension brews as Ogiue scoffs at the idea of cosplay, and Ohno finds Tanaka's secret stash of costumes for the other Genshiken girls. Caught in the middle with the photo shoot only minutes away, Kasukabe hatches a scheme to smooth things over, and even get Ogiue to try something she's never done before...
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