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.

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.

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.

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.

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.

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.

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.

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?

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.

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.

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?

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.

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?

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.

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?

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.

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.

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?

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.

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