Director Yamamoto heads the Japanese branch of ARCAM Corporation, an organization dedicated to securing dangerous ancient relics called OOPArts. His duties involve overseeing operations and managing key personnel within the division.

A key element of his past is discovering Yu Ominae, a former child soldier for the covert unit COSMOS. Recognizing both Yu's potential and troubled history, Yamamoto took him in as a ward. He personally trained Yu in military tactics, guerrilla warfare, and field operations, preparing him to become a Spriggan operative—ARCAM's elite agents. Yamamoto then served as Yu's primary handler, directing his missions and deployments.

He commands decisively during critical incidents, such as recalling Rie Yamabishi to Japan due to her past connection with Yu. When COSMOS forces assaulted ARCAM's Japanese headquarters, Yamamoto actively fought in the defense, coordinating efforts to repel the attackers.

His role intensified during the South Pole mission, where ARCAM forged an uneasy alliance with the rival Trident Corporation to investigate the Antarctic Shrine and its artifact, the Fire Snake. Initially collaborating with Trident executive Henry Garnum, Yamamoto ultimately orchestrated Trident's betrayal. He aligned with ARCAM personnel to defeat Trident's Antarctic forces and played a key role in containing the Fire Snake before it could unleash catastrophic damage.

Through these events, Yamamoto consistently prioritizes ARCAM's core mission of preventing ancient artifacts from being weaponized, placing this objective above temporary alliances with rival organizations.