As another school year begins drawing to a close, the third-year high school students move steadily toward the next milestone of their lives: graduation. Among them are Mio Natsume, a girl burdened with lingering feelings; Hazuki Morikawa, a member of the concert band but distant from the others; and Haruto Souma, an athlete obsessed with baseball. Meanwhile, second-year student Ena Komiya seeks to revive the photography club to its former glory, refusing to let the organization be disbanded. Though this group lacks a strong connection with one another, their lives suddenly cross paths with the arrival of a third-year transfer student. While a transfer so close to graduation is unusual for most, it is business as usual for Eita Izumi. Due to his father's work, he has never been able to stay in one place for very long. But as luck would have it, their most recent relocation has returned Eita to his hometown for his final semester of high school. For better or worse, it also sparks the rekindling of old relationships left behind in the past. With graduation already causing its own share of anxieties, Eita's sudden arrival brings these students' carefree days to an abrupt end. Long-forgotten memories, deeply buried emotions, and inspiring new passions—everything is brought to light in their bittersweet final semester.

As with its prequel, Zoku Natsume Yuujinchou is about Takashi Natsume, a boy who has had the ability to see youkai since he was young, and his bodyguard youkai Madara, nicknamed Nyanko-sensei. Natsume attempts to return names written in his Book of Friends (which he inherited from his grandmother Reiko) to youkai in his village. Throughout these adventures, he meets some youkai that are friendly, some that want to steal the Book, and some that want to kill him, as Natsume learns about himself and his relationship with these mysterious beings along the way.

They say that the more things change, the more they stay the same, and those words could not be more true for the student council of Ousai Private Academy. Though an entire year has passed—bringing the senior members to their final year of high school—not much has changed. President Shino Amakusa is just as perverted as ever, Secretary Aria Shichijou still refuses to put on a pair of panties, Treasurer Suzu Hagimura has yet to grow an inch, and Vice President Takatoshi Tsuda is still stuck as the straight man to their crazy antics. Of course, limiting the fun to a four-way might get a little stale; although the group still messes around with the Judo Club and the Newspaper Club, more girls have come to get in on the excitement. Takatoshi's sister Kotomi, a new student at Ousai, is as perverse as the president, while Uomi, the aloof student council president of the nearby Eiryou High School, fits right in with the insanity at Ousai. With loads of absurdity and sexual humor that keeps on coming, Takatoshi needs to harden up if he is going to keep up with all the madness around him.

Following their success in the qualifying round for the Kansai regional competition, the members of the Kitauji High School concert band set their sights on the next upcoming performance. Utilizing their summer break to the utmost, the band participates in a camp where they are instructed by their band advisor Noboru Taki and his friends who make their living as professional musicians. Kumiko Oumae and her friends remain determined to attain gold at the Kansai competition, but trouble arises when a student who once quit the band shows interest in rejoining and sparks unpleasant memories for the second-year members. Kumiko also learns about her teacher's surprising past and the motivation behind his desire to lead the band to victory. Reaching nationals will require hard work, and the adamant conviction in each student's commitment to the band will be put to the test.