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.

After separating from Lenny and Titan, Takt and crew continue their journey under the blazing sun. During their trip, they end up fighting some D2s and end up bringing a train on the transcontinental railroad to a sudden stop. They then see a Musicart in white armor and a Musicart with a bewitching smile. The man accompanying the two Musicarts is named Shindler and calls himself the Top Conductor of the New York Symphonica.

Takt and crew finally reach their destination of New York. They reunite with Charlotte, Anna's older sister, who works for the Symphonica's technological development department. Charlotte begins to examine Destiny. Who is an incomplete Musicart. But then, Anna realizes something is wrong with Takt. The mark on Takt's right arm starts to spread to the rest of his body, and...

Lenny remembers his own past. Lenny recalls someone very dear to him. Everything leading up to today was so that he could do everything he could to do what he had to do. Lenny heads to the meeting point along with Titan so they can tell Takt and Destiny everything. But someone rather unexpected was waiting for them.

A giant Black Night Siderite starts to stir as Sagan hums a certain melody. The Black Night Siderite that grows as big as a tree starts to swallow up the New York Symphonica. Sagan has finally made his move to make his ambitions come true. As Takt and Destiny witness this eerie spectacle, they find out that Anna and Charlotte are still inside the Symphonica.

Destiny is terribly cruel. But no matter how much misfortune the gods torment me with, I will face my destiny. Because of that, I fought, and I fought, and I fought some more... And then, I finally found my answer. There truly was joy beyond the pain. Now, it is time for the performance to begin. I shall now wring destiny's neck. "From a certain man's memoirs"