Koji Takahashi leads Branch, a covert A.D. Police division operating outside standard protocols to investigate crimes by rogue androids called Boomers. His college friendship with Basil "Buzz" Nikvest led him to recruit Buzz into Branch after an accidental shooting incident, forging their professional dynamic within the unit.

Initially principled, Takahashi's integrity erodes under career pressures and the morally gray demands of their work. The narrative marks his ethical decline, indicating he is no longer the "clean" man he once was and implying involvement in dubious actions.

Five years after the second OVA's events, Takahashi vanishes mysteriously. His disappearance triggers Branch's investigation into a surge of anti-Boomer terrorism, exposing a conspiracy to destabilize human-Boomer relations. The probe implicates Takahashi as either a target or participant in the plot.