Kotaro Takamiya and his younger brother Teppei grew up on Kamui Island following their parents' death. Demonstrating exceptional scientific talent early on, he earned acclaim as a "boy genius" in academic circles. During his youth, he built a small laboratory within an island cave, creating a sanctuary for both brothers. At age eleven, supported by the Machine Empire, he departed for robotics studies in Berlin, Germany, separating from Teppei for years.

He rose as a leading expert in robotic biology and biorobotics, drawing the Machine Emperor’s attention through revolutionary theories on autonomous robot behavior. Five years after leaving Kamui Island, he traveled to Mechatopia in Peking, China, as a guest speaker at an international robotics convention, intentionally arranging to reunite with Teppei there. During his presentation, Machine Empire soldiers Aramis and Metalface abducted him, transporting him to the Empire’s hidden fortress, the Area, in the Gobi Desert.

Inside the Area, Kotaro was confined in the subterranean prison Underhell. Major Aramis disclosed he was chosen for his expertise, particularly his research on robots developing self-directed actions. His primary task became researching Raffaello—an ultimate B't undergoing uncontrollable evolution threatening global destruction. During captivity, he witnessed Warden Marcello accidentally drop a vial containing Raffaello’s cell, escalating containment risks. Imprisoned, he bonded with fellow captives including Marcello, whom he comforted during a mine oxygen crisis; tearfully writing the sunlight formula, he acknowledged his scientific knowledge’s limits in saving lives.

His research focused solely on destroying Raffaello. In the B't X Neo storyline, he collaborated with German scientist Dr. Lisa Maria Stein to solve equations halting Raffaello’s evolution, their partnership including a semi-romantic subplot. His intellectual contributions proved pivotal in devising countermeasures against Raffaello, aligning with the mission to thwart the Machine Empire’s catastrophic plans.

At Neo’s climax, he shared the protagonists’ fate when Teppei activated Kamui Island’s sun fragment to destroy Raffaello. Kotaro perished in the conflagration consuming the Area. This conclusion diverged from the manga, where he survived the final space battle and resumed life with Teppei. Neo’s epilogue perpetuated his legacy through Karin, who recounted his story as a foundational legend for the reformed Machine Empire.

Kamui Island’s meteorite origin and its subterranean "piece of the sun" remained intrinsically linked to his backstory and the series’ resolution. His character consistently exemplified the ethical responsibilities of scientific advancement amid themes of sacrifice and redemption.