Yamato Mikogami is the son of Dr. Masahiko Mikogami, founder of the defense organization ASY. He pilots ASY's mechanized units, specifically the Type-1 Ginko—one of five Gousen mechs developed to protect Japan following its military integration into the United Nations. His duty pits him against the Shiromorishu, an occult group seeking vengeance after losing spiritual control over Japan.

Yamato's initial dedication to ASY's mission falters as he observes his father's secretive actions and the organization's morally ambiguous tactics, breeding doubt about ASY's true nature as a force for good. This internal conflict deepens when he encounters Rouran, a mysterious fairy-like being whose actions and origins challenge the perceived binary of the conflict. Rouran compels Yamato to question the ethics of ASY's operations and his father's motivations.

His familial ties further complicate his path. His younger sister, Mahoro Mikogami, initially presents unwavering support. However, Mahoro's own enigmatic background culminates in her revelation as Banka—a deceptive Shiromorishu agent wielding supernatural abilities. This betrayal infuses Yamato's journey with emotional turmoil and strains their bond, intensifying his isolation.

Throughout the series, Yamato evolves from a loyal soldier into a conflicted individual wrestling with disillusionment. His interactions with Rouran and exposure to ASY leadership's darker aspects fuel this transformation. The narrative uses him to explore themes of loyalty, identity, and the blurred moral lines between opposing forces where neither side claims clear superiority.