Colonel Matoi Shinkai commands the Kishin Corps, an elite Allied military unit combating extraterrestrial threats in an alternate World War II invaded by aliens. He holds full authority over the unit’s operations and personnel, directing deployments of giant Geo-Armor robots engineered from captured alien technology. His strategic responsibilities include deciding whether to use or destroy alien artifacts to prevent their seizure by hostile Axis powers—specifically the Nazis and Japanese Kanto Army—who seek to weaponize this technology.

Shinkai operates with unwavering commitment to the Kishin Corps’ mission: protecting humanity from alien invaders and Axis exploitation of alien tech. This often forces him into difficult choices, such as destroying alien devices rather than risking enemy capture. His leadership directly opposes the Kanto Army and Nazi forces, who view the Kishin Corps as obstructing their objectives.

Throughout the conflict, Shinkai interacts with key individuals like Taishi, a teenager safeguarding a vital alien control device, and manages personnel including Yoshimitsu "Bill" Suguro. He also oversees alliances with defectors such as Eva Braun, who affiliates with the Kishin Corps. Time’s passage visibly ages Shinkai across the series, yet his leadership remains a constant as the unit battles combined alien and Axis threats.