Junjou Romantica follows three intertwined boys-love romances that unfold across the same world. At the center is Misaki Takahashi, a high school student who comes home to find his older brother being fondled by Akihiko Usami, a bestselling novelist and his brother's best friend. When Akihiko becomes Misaki's private tutor, Misaki's distrust grows after he stumbles upon the author's latest boys-love novel, but their uneasy closeness slowly turns into something far more complicated.
The second story focuses on Hiroki Kamijou, a university teacher of classical literature and one of Akihiko's friends, who is recovering from a painful failed romance. While he is on the brink of a breakdown, he meets Nowaki Kusama, a student seeking help for an upcoming exam. Hiroki repeatedly refuses, yet eventually agrees to tutor him, and the two begin to uncover more about each other.
The third romance follows wealthy teenager Shinobu Takatsuki, who learns that his older sister has divorced Hiroki's coworker You Miyagi. Shinobu decides he wants to date Miyagi because the man once saved him from a robbery three years earlier, but Miyagi wants nothing to do with him and tries to drive him away. Even so, Shinobu refuses to give up on what he believes is a destined relationship.
Across these connected couples, Junjou Romantica presents comedy, longing, and melodrama through three distinct love stories that together define the franchise.