Four years had passed since Sagan's called a truce with the D2s. Music was still taboo throughout the world, and melodies ceased to be heard. Somewhere in America, which was now a wasteland, a little boy who grew up not knowing what music is hears the melody from a piano. The one playing it is a young man with black hair named Takt. And then, a deformed creature known as a D2 and a girl named Destiny, who is armed with a sword, appear as though they were lured in by the melody.

It all began ten years ago. D2s attacking Boston, a blood-soaked concert hall: The incident known as the Boston Tragedy. The conductor who lost his life in that tragedy was none other than Kenji Asahina, Takt's father. After losing his father, the boy decides to devote himself to playing the piano and he lets his rage play through his melodies. The one who took care of him was a girl named Cosette, who looked just like Destiny.

Cosette transformed into the Musicart named Destiny. Destiny proclaims that her mission is to eliminate the D2s. Destiny bestows a conductor's baton upon Takt, and he uses his Conductor powers for the first time. And then, they are confronted by two individuals: Lenny and Titan. They are an official Conductor and Musicart from the New York Symphonica, which was the strategic headquarters to fight the D2s.