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.

In ancient Disboard, Riku is an angry, young warrior intent on saving humanity from the warring Exceed, the 16 sentient species, fighting to establish the One True God among the Old Deus. In a lawless land, humanity's lack of magic and weak bodies have made them easy targets for the other Exceed, leaving the humans on the brink of extinction. One day, however, hope returns to humanity when Riku finds a powerful female Ex-Machina, whom he names Schwi, in an abandoned elf city. Exiled from her Cluster because of her research into human emotions, Schwi is convinced that humanity has only survived due to the power of these feelings and is determined to understand the human heart. Forming an unlikely partnership in the midst of the overwhelming chaos, Riku and Schwi must now find the answers to their individual shortcomings in each other, and discover for themselves what it truly means to be human as they fight for their lives together against all odds. Each with a powerful new ally in tow, it is now up to them to prevent the extinction of the human race and establish peace throughout Disboard.

Yukihisa Matsuda, principal conductor of the Rising Star Orchestra, arrives in Paris to perform Wagner's Tannhäuser Overture as a guest conductor for the Recyl Symphony Orchestra. When Matsuda overhears the orchestra members praising Shinichi Chiaki, the budding Japanese conductor of the Roux-Marlet Orchestra, he can barely contain his contempt at there being another Black-Haired Noble in the same city. Freshly dumped by his mistress following the performance, Matsuda catches Chiaki and takes him out to drink under the pretense of discussing career. But much to Chiaki's chagrin, the subject soon turns to Chiaki's own special someone.

Shinichi Chiaki is quickly making a name for himself as the principal conductor of the revitalized Roux-Marlet Orchestra, and Megumi Nodame Noda has made leaps and bounds as a pianist at the Conservatoire de Paris. However, tensions mount between the two as Nodame feels left behind by Chiaki's growing success and his close friendship with legendary piano prodigy Rui Son. Disregarding her teacher Professor Charles Auclair's advice, Nodame enters another piano competition in an attempt to jumpstart her own performance career. Meanwhile, those around Chiaki and Nodame are at their own crossroads. Rui begins to doubt herself after hearing Nodame's playing and being denied tutelage from Auclair; Maestro Franz von Stresemann faces the reality of his mortality; pianists Yunlong Li and Tatiana Vishneva feverishly prepare for a competition, while the latter also struggles with her growing feelings for oboist and fellow student Yasunori Kuroki. As Chiaki, Nodame, and their friends continue on their respective journeys, they must not only strive to stay true to themselves, but also remember where it all started.