John D. Kunugi is a member of Spitzbergen, an organization opposing cybernetic enhancements called Extensions. Despite this membership, he secretly collaborates with Berühren Corporation, as Spitzbergen's terrorist activities increase public demand for Berühren's Extension technology and boost their profits.

Physically, Kunugi possesses short blond hair that often covers his blue eyes and facial scars, and he wears a distinctive white coat. He operates as a combatant wielding a needle gun capable of restricting an opponent's movement or enhancing their power, even in non-Extended individuals. During a confrontation with Juzo Inui, Kunugi notes the difficulty of facing an Over-Extended opponent and strategically targets allies to gain leverage.

Kunugi captures Tetsuro Arahabaki and delivers him to Spitzbergen representative Andy Wachowski. Wachowski later releases Tetsuro as part of a deal to use the Harmony device against Berühren. Kunugi expresses skepticism about Wachowski's leadership, particularly concerning Victor Steinberg's inclusion in Spitzbergen. He views Victor's involvement as a mistake due to Victor's deep ties to Extension development—the very technology Spitzbergen aims to eradicate. Kunugi also questions whether Wachowski has undisclosed objectives beyond their stated mission.

His allegiance to Berühren surfaces during conflict with Juzo. Kunugi reveals sponsorship by Hugh Cunningham, a Berühren executive, explaining that terrorist acts create market demand for Extensions. Kunugi's role includes delaying Juzo to enable Berühren agent Pepper's assassination attempt on Wachowski. When the assassination fails, Kunugi attempts to escape but encounters Cronen von Wolf, a former training comrade. After a brief skirmish, Kunugi exploits a distraction caused by Juzo and Seven's battle to flee the scene.