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.

Takt and Destiny learn how to fight properly from Lenny and Titan as they continue to make their way to New York. However, Takt and Destiny still have a hard time being in sync. They then coincidentally run into Lenny's old buddy Jonathan. Jonathan then leads them around his home, Las Vegas.

Takt and crew stop by a certain town. All of the young people had fled the town, leaving only the elderly. The residents happen to ask Anna and Destiny for help. Meanwhile, Takt wandered around town on his own and happens to hear a melody quietly resonating from an old bar. It was definitely the sound of music.

Anna and Destiny happen to see a town destroyed during their travels. D2s are awakening everywhere and attacking various towns and people, reverting the world back to four years ago, before Sagan's Declaration. As the threat from the D2s grew, Takt was obsessing over something. With a blank staff notation in front of him, Takt plays an imaginary keyboard as he desperately tries to create something.

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...

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.