This world has gone through many Dusks, and is slowly nearing its end. Within this world, in the western reaches of the "Land of Dusk," there was a nation that prospered thanks to its use of alchemy. There, in order to survive the eventual arrival of the "Dusk End," the people devoted their efforts to rediscover and recreate lost alchemic technologies. Rediscovered technology from the past era was gathered in the alchemy research city known as "Central," where research was conducted on how to halt the advance of the twilight. One of the heroes is a young man who researched alchemy in Central, the other a girl living in a small town on the frontier. This girl's name is Escha. In the process of using her knowledge of ancient alchemy to help others, she was assigned to the Development Department. The young man's name is Logy. Having learned the newest alchemic techniques in Central, he requested a transfer to this understaffed town to make use of his abilities, and meets Escha when he is assigned to the Development Department as well. The two make a promise to use their alchemy together, and bring success to the Development Department.

Not far from the town of Domina lives Shiloh, a boy who keeps hearing a voice in his dreams about a mission he must fulfill. But what mission could he be needed for remains unknown. That all changes when he meets two Jumi, a race that’s hunted for their unique gemstones, as a sudden outbreak of attacks against the Jumi occurs. His dream, his quest, becomes clear—help the Jumi and their gemstones!

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. [Written by MAL Rewrite]

Hayate Ayasaki's misfortune continues to hand him the short end of the stick. Now settled into his routine at the Sanzenins' mansion and Hakuou Academy, the butler continues to work as hard as ever in caring for his young mistress Nagi while studying the school's grueling curriculum—all on top of trying his best to survive the multitude of troubles that life relentlessly pushes onto him. The unintentional chick magnet's life is far from quiet, forced to deal not only with Nagi's yet unnoticed infatuation with him, but also the evergrowing string of accidentally seduced girls—most notably, the exceptionally plain Ayumu Nishizawa, a friend of his before he became a butler, and the diligent Hinagiku Katsura, Hakuou's student council president. While one struggles to gain his affection and the other desperately tries to deny her own, both the girls are going to make the boy's life a little more complicated than it already is. [Written by MAL Rewrite]