Yuya Kanzaki arrives as a transfer student shrouded in quiet mystery, his detached maturity setting him apart from classmates. Behind his unreadable composure lies a pivotal link to the cataclysmic "Burst"—a disaster triggered by a doomed experiment to forge artificial life, annihilating Kurobe Gorge and unleashing synthetic entities called Matter.

Unveiled as Toshihide Yura, a scientist who perished in the Burst’s genesis, his preserved brain was transplanted into an artificial vessel dubbed "Duplicate One" by colleague Susumu Kurose. This rebirth binds him to the crisis as both architect and penitent, driving his resolve to lead protagonist Aiko Tachibana to Primary Point, the disaster’s origin.

His guarded exterior belies a turmoil of remorse and purpose. Interactions with Aiko expose her artificial form and the captivity of her original consciousness within the Matter, intertwining their quests. While steering the Divers—specialists navigating the quarantined zone—he leverages scientific expertise to outmaneuver threats, yet secretive tactics strain alliances.

The journey forces reckoning with ethical dilemmas of synthetic existence and the weight of past choices. His final push to halt the Burst converges with Aiko’s struggle to reclaim her humanity. Though the crisis concludes, his destiny lingers unresolved amid the aftermath. The epilogue leaves his fate unspoken, while Aiko’s autonomous new life echoes his legacy—a testament to identity’s fragility and renewal.