Jubei Kibagami wanders feudal Japan as an itinerant swordsman-for-hire. After a past betrayal left him masterless, he has no more patience for warring political factions and their schemes. Unfortunately, both past and political intrigue collide when he meets and saves a female ninja named Kagero from a man with the ability to make his body as hard as stone. The sole survivor of a ninja clan, Kagero continues her team's last mission: investigate a mysterious plague that wiped out an entire village. Jubei wants nothing to do with this, but the stone-like man's allies, a group of ninja with supernatural powers known as the Devils of Kimon, make that option difficult. To make matters worse, a government spy poisons Jubei, promising him an antidote if he can unravel the true intentions of the Devils of Kimon and their connection to the plague. The trail leads to shadow leaders, a plot to overthrow the government, and a man that Jubei thought he would never see again.

The members of the Gourmet Guild—Yuuki, Kokkoro, Pecorine, and Karyl—continue to scour the world in pursuit of their goal to seek out all delicious food in existence. However, as their adventures progress, the mysteries behind Yuuki's memories, Karyl's allegiance, and Pecorine's heritage begin to come together—seemingly forming the truth that makes up the world's very foundation.

Sixteen-year-old Yuuki Hase finally finds the courage to speak to his crush and ask her if she wants to become friends. The object of his affection, Kaori Fujimiya, is a quiet and reserved girl who cuts herself off from everyone and does not spare him the same blunt rejection she gives everybody else. Some time after, Yuuki finds her eating lunch on the roof where she secludes herself during break. He decides to start meeting with Kaori every day in the hopes of beginning to understand her better. The more time they spend together, the more she begins to open up to him. However, nearing the end of the week, she starts to push him away once more. It is then revealed to him the reason for Kaori's cold front: at the end of the week, her memories of those close to her, excluding her family, are forgotten, as they are reset every Monday. The result of an accident in middle school, the once popular and kind Kaori is now unable to make friends in fear of hurting the people dear to her. Determined to become more than just one week friends, Yuuki asks her the exact same question each Monday: Would you like to be friends? Because he knows that deep down, Kaori wishes for that more than anything.

The second part of Junjou Romantica continuing the story.