Sixth grade student Hiromi Nozawa leads a troubled life. With her parents frequently absent due to work, one of her only companions is her talking dog, Junkers. Though Hiromi puts on a brave face for the public, the stark reality is that she is heavily stressed, and she shares this side of herself only with Junkers. After hearing that her parents are considering divorce, Hiromi's stress reaches an all-time high; at this time, Junkers reveals that he has the ability to make three miracles occur. Given the potential of this newfound power, Hiromi must wish carefully—as obtaining what she thinks she wants may end up hurting those she cares about most.

High school student Misaki Takahashi returns home to see his older brother being fondled by an unknown man. Bewildered by such a sight, Misaki finds out that the stranger is actually Akihiko Usami, a popular novelist and his brother's best friend. With the two of them slowly becoming acquainted, Akihiko ends up as Misaki's private tutor. However, after stumbling upon the author's latest boys-love novel, Misaki becomes uncertain whether or not to trust Akihiko regarding his friendship with the student's brother. Elsewhere, Hiroki Kamijou, a university teacher of classical literature and Akihiko's friend, is grieving a failed romance. While on the edge of a mental breakdown, he meets student Nowaki Kusama, who wants his help for an upcoming exam. Despite denying Nowaki's request numerous times, Hiroki eventually lends him a hand. As the two get closer, more revelations about the student are made. Furthermore, when wealthy teenager Shinobu Takatsuki finds out that his older sister has divorced Hiroki's coworker You Miyagi, he immediately wants to date the same man—as he saved Shinobu from a robbery three years prior. Even so, You does not feel the same way and attempts to scare him off. However, the educator soon realizes that Shinobu will do anything for their destined romance. Junjou Romantica collects three love stories, narrating every couple's romance.

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!