Colonel Muto is a high-ranking officer within the Imperial Japanese Army who serves as a direct superior to the protagonist, Lieutenant Sakuma. He is an older, stern-looking man with a dark mustache, usually seen in a formal military uniform and often carrying a katana. As a colonel, he holds significant authority and represents the conventional, rigid mindset of the military establishment during the pre-World War II era.

Personality-wise, Colonel Muto embodies the traditional, uncompromising values of the Imperial Army. He is pragmatic to a fault, more concerned with saving face and adhering to strict protocol than with the practical outcomes of a mission. This is demonstrated when he sends Sakuma on a mission to search the home of John Gordon, an American spy suspect. The search is not genuinely intended to succeed; Muto had previously conducted the same search and found nothing. Rather than accept responsibility for that failure, he assigns the task to the inexperienced Sakuma to serve as a scapegoat for the anticipated embarrassment. This action reveals a deeply ingrained ego and a tendency to prioritize his own reputation over the lives and careers of his subordinates.

The character's motivations are rooted in a strict adherence to militaristic nationalism. Muto cares deeply about the sanctity of symbols like the imperial portrait, which, due to religious reverence, was a taboo object to examine or touch. His immediate reaction after Sakuma’s search is not relief at the discovery of evidence, but a frantic question about whether the portrait was disturbed. He demands severe punishment for the spies and a recovery of stolen intelligence, viewing espionage through a lens of honor and retribution rather than strategic subtlety.

In the story, Muto serves as an antagonist foil to Lieutenant Colonel Yuuki, the head of the D Agency. Where Yuuki values long-term national security and pragmatic deception, Muto values immediate military expansion and public prestige. When Sakuma returns with a report that Yuuki has resolved the situation by turning the American spy into a double agent and leaking false information, Muto is not relieved but furious. He views Yuuki's success as a personal defeat because it sidelines his authority and contradicts his view of how the empire should operate. Consequently, his attempts to use Sakuma as a tool to undermine the D Agency backfire, highlighting the obsolescence of his rigid thinking in the shadow war of intelligence.

Colonel Muto has a key relationship with Lieutenant Sakuma. He views Sakuma as an expendable pawn, a loyal soldier he can sacrifice to shield himself from failure. The pressure Muto places on Sakuma is so severe that it drives the young lieutenant to nearly commit seppuku (hara-kiri) to atone for his perceived failure before realizing the colonel's betrayal. Their dynamic illustrates the clash between blind loyalty to a flawed system and the emergence of individual critical thought.

There is little to no character development for Colonel Muto; he remains a static representation of the old military guard. His primary function is to be outmaneuvered by the D Agency, proving that traditional authority is ill-equipped to handle modern espionage. His notable abilities lie not in physical combat but in his authoritative position and his understanding of military bureaucracy. He uses his rank to wield power over subordinates and to attempt manipulation of the army's chain of command against Yuuki. Possessing a katana and wearing gloves, his appearance reinforces his adherence to strict militaristic discipline and tradition.