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!

OVAs that come with the limited premium edition of volumes 16 and 20 of the manga series.

After conquering the galaxy, mankind has reached its apex and is now on a steady decline. The resources of the universe are diminishing, and around 500 billion humans begin to return home to Earth. Thus begins a war between the various factions of humans for control of the planet. Eventually, an authoritarian government known as the Gaia Sanction prevents the re-population of Earth. Captain Herlock was one of the Elite Wing who was tasked by the Gaia Sanction to defend the Earth. His fleet of ships was unstoppable under his command. However, the Gaia Sanction allows a diplomatic elite to immigrate to Earth, which angers Herlock. He goes rogue and fires upon the diplomats and the rest of his fleet. He decides to unleash dark matter on the planet to make it uninhabitable, but also becomes engulfed in it which immortalizes him. One hundred years have passed, and the legendary Captain Herlock is still at large, with only the Arcadia under his control. The Gaia Sanction continues with their plans for control over the Earth, while hiding its true state. But Captain Herlock is preparing for one final showdown with them, which will determine the fate of the world!

Three hundred years ago, in the frigid land of Siberia, Jubei Yagyu engaged in a fierce battle with Kitaretsusai of the Northern Yagyu clan. The duel was costly, as his daughter Freesia was frozen in suspended animation. As a result of global warming in the present day, Freesia breaks free from her icy grave and moves to Japan as a middle school transfer student, where she befriends Jiyuu Nanohana. Little does Jiyuu know that Freesia is targeting her to acquire the coveted Lovely Eye Patch, which Freesia believes is rightfully hers.