Makoto Yamamoto serves as the first officer aboard the Soyokaze. Hailing from a strict military family, he embodies a strong adherence to rules and professionalism. He persistently imposes order and discipline on the crew, constantly clashing with Captain Tylor's lax command style and unconventional methods. This friction generates significant stress, leading to regular visits to the ship's medic for tranquilizers and use of a neuro-cleanser. Though viewing Tylor as incompetent, Yamamoto feels torn between his duty to report the captain's inadequacies to United Planets Space Force (UPSF) leadership and the military code demanding loyalty to his commanding officer. He harbors a deep ambition to command his own vessel.

Beneath his disciplined exterior, Yamamoto displays contradictions. He exhibits emotional vulnerability, crying during sentimental moments and showing nervousness around attractive women. Passionate speeches or displays of resolve easily sway him, causing him to abandon protocol. A notable incident involves him declaring "Now I'll show them how a real captain acts!" – a statement incorporating a pun on his first name "Makoto," meaning "real" or "true".

Throughout the series, Yamamoto undergoes significant development. Initially exasperated by Tylor, he gradually adopts some of Tylor's unconventional approaches. By the conclusion, he develops respect for Tylor and fully supports his captaincy of the Soyokaze, believing Tylor is irreplaceable. He declines a promotion to captain of the new ship Aso to remain under Tylor's command.

In later manga *Love & War*, set after the OVA events, Commander Yamamoto serves as Tylor's staff officer and adjutant aboard the battleship Omi. He participates in a time-travel mission to the Raalgon Empire's past, indicating continued service alongside Tylor and further career progression within the UPSF.