Jiyu Nanohana is an ordinary schoolgirl until she runs across a scatterbrained 300 year old samurai who tells her that she is the reincarnation of Yagyu Jubei. With the help of the "Lovely Eyepatch" she transforms into the legendary swordsman whenever she needs to use his awesome fighting ability, which she needs to do quite often as a rival clan is dead set on conquering Yagyu to satisfy an old family grudge.

Misaki Takahashi is a regular high school student who is preparing for his university entrance exams. In order to reduce the stress of studying, or so he hopes, he accepts the help of his older brother's best friend, and famous author, Akihiko Usami. However, Masaki is about to find out that Usami's books are of a very naughty genre, and that there may be something naughty waking up inside Masaki as well. Junjou Romantica also follows the story of two other couples loosely connected to Masaki and Usami's "Romantica." Egoist shows the very passionate, but often complicated, relationship between university professor Hiroki Kamijou (whose life has reached an all time low) and paediatrician Nowaki Kusama, who falls for Hiroki at first sight and would do anything to make him happy. The third story, "Terrorist," shows just how obsessive love can become when rich eighteen-year-old Shinobu Takatsuki finally discovers something that he cannot have so easily—the literature professor You Miyagi. There is passion abound as these three couples try to achieve their goals in life while also falling into temptation and anguish with their partners.

The second part of Junjou Romantica continuing the story.

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!