After living together for three years, Misaki Takahashi and Akihiko Usagi Usami's relationship has been progressing smoothly. However, all great relationships have problems, and theirs is just beginning. With a new rival on the horizon, Usagi worries about Misaki's feelings towards him. Meanwhile, Ryuuichirou Isaka has always loved to intrude on Misaki and Usagi's love life, but his own love life hasn't been all smooth sailing—Isaka and his secretary Kaoru Asahina have been dating for a few years; however, Asahina prefers to keep their professional and private lives separate, often leading to troubled waters between them. As for Nowaki Kusama and Hiroki Kamijou, now that their careers are finally taking off, they hardly see each other anymore. With the time they spend together lessening, doubts and insecurities threaten to creep in between them. On the other hand, the 17-year age gap between Shinobu Takatsuki and You Miyagi has been a constant barrier in their relationship, but as they learn more about each other, their self-consciousness continues to fade. The beloved couples of Junjou Romantica, Junjou Egoist, and Junjou Terrorist are back again, this time with a new addition: Junjou Mistake!

One day, high school student Michio Kaga attempts to start a strange online game he found while browsing the internet. Instead, he gets transported to a rural village in the game's world, equipped with special skills and an overpowered sword. After collecting his thoughts, he finds himself battling against bandits and soon realizes that he cannot log out. Resigning himself to fate and accepting this reality, Michio sets out on a journey—enjoying his new life, conquering dungeons to earn money, and building a harem to satisfy all his manly desires.

Rikuo Uozumi has all but resigned himself to a bleak future, aimlessly working at a convenience store in Tokyo after graduating from college. His monotonous life is interrupted when the peculiar Haru Nonaka makes a lively appearance, frequently dropping by his workplace to befriend him. When Rikuo learns that an old college friend and crush, Shinako Morinome, has moved back into town, he reaches out to further their relationship. Unbeknownst to Rikuo however, Shinako is carrying painful memories from her past that were holding her back from accepting his feelings. Meanwhile, as Haru continually opens up to Rikuo, he discovers that she, much like him, is living by herself and wants to step out of her comfort zone into an uncertain future. The past lingers long in the mind, and the future remains elusive. At a crossroads along their intertwined paths, these three experience what it means to let go of their feelings of yesterday and embrace the change that tomorrow brings.

The spin-off anime to Gintama follows Ginpachi Sakata as a teacher in Gintama High School.