Continuing where the first season left off, the sudden increase of Thanatos with the disappearance of the Aube Hunters has now left Arcadia in ruin. Desperation reigns high as the Religious Organization fights to battle the Thanatos. Six months had already past since Hidamari mansion burned to ashes, the Aube Hunters, once hailed as heroes, is now blamed for the appearance of Thanatos. Nevertheless, hope still exists for the reappearance of the Queen's Egg one day, who will become the savior of Arcadia. Unknown to many however, the Aube Hunters have actually been silently waiting for the awakening of Angelique, who has been asleep the entire time.

The Taishou era didn't end in 15 years, but went on for another 25. In order to protect her waning family, a girl resolves to marry a man she doesn't even know the name of. However, just before the marriage was to take place, the girl's younger brother mysteriously committed suicide by self-immolation and was found holding an old book in his hands. Appearing before the bewildered young girl was the Imperial Library Intelligence Asset Management Bureau, more commonly referred to as Fukurou. According to these men, there exists Maremono, which are books that greatly affect their readers. On top of that, ever since the incident involving the girl's younger brother, she unwittingly gains the ability to see Auras (the sentiments of the Maremono which manifest as bright lights and are usually invisible to humans). It was as though fate were trying to drag the young girl in its flames. And then, even though apprehensive, the girl chooses to venture outside her bird cage. Jealousy, hatred, scorn, compassion, and love. What awaited the girl was the darkness of betrayal that had already begun to bewitchingly inlay the imperial capital. Toyed by and swayed within that darkness, will the young girl finally reach the truth after her struggles, or...? (Source: MAL News)

Shinichi Chiaki is a first class musician whose dream is to play among the elites in Europe. Coming from a distinguished family, he is an infamous perfectionist—not only is he highly critical of himself, but of others as well. The only thing stopping Shinichi from leaving for Europe is his fear of flying. As a result, he's grounded in Japan. During his fourth year at Japan's top music university, Shinichi happens to meet Megumi Noda or, as she refers to herself, Nodame. On the surface, she seems to be an unkempt girl with no direction in life. However, when Shinichi hears Nodame play the piano for the first time, he is in awe of the kind of music she creates. Nevertheless, Shinichi is dismayed to discover that Nodame is his neighbor, and worse, she ends up falling head over heels in love with him.

Shinichi Chiaki conquers his fear of flying, and Megumi Nodame Noda's exceptional performance at a piano competition earns her an invitation to study at the prestigious Conservatoire de Paris. The pair go to Paris together to take the next step in their careers: Chiaki as a new rising conductor under the wing of the great maestro Franz von Stresemann, and Nodame as a pupil of the esteemed piano professor Charles Auclair. But, of course, the music world is much bigger than the two of them could have ever imagined. Chiaki and Nodame, alongside old friends and new rivals, must fight and persevere to reach the dazzling musical heights that await them while never losing sight of what matters most.