In a near-future Japan, civilization has collapsed following a nuclear war, a series of natural disasters, and the corrupt governance that led to a violent revolution. Society has regressed to a state comparable to the late 19th century, and the nation has fractured into three warring superpowers: Yamato in the west, Buo in the east, and Seii in the north. This new era, known as the Sangoku period, is defined by a relentless military and political struggle for total control over the remnants of Japanese land.

The story centers on Aoteru Misumi, a humble former agricultural officer living a quiet life in the countryside of Ehime within the nation of Yamato. After his wife, Saki, is brutally killed by a corrupt official from the ruling Taira clan, Aoteru vows to fulfill his promise to her of creating a peaceful world. Uniquely, he is not a physical fighter; his only weapons are his vast knowledge, sharp insight, and exceptional eloquence. He aims for nothing less than the complete reunification of Japan and begins his rise as a genius military strategist.

The primary antagonist in Yamato is Denki Taira, the Minister of the Interior and a dictator who poisoned the previous emperor to control the government. To achieve his goal, Aoteru travels to Osaka, the capital of Yamato, to take a difficult exam given by General Mitsuhide Ryumon, a noble commander of the Borderland forces. There, he meets Yoshitsune Asama, a skilled and ambitious young man from a distinguished family who excels in martial arts. Their contrasting personalities—Aoteru’s calm logic versus Yoshitsune’s arrogant ambition—immediately create a dynamic rivalry as they both prepare to face the challenges of the exam together.

The narrative explores the intricate power struggles, shifting alliances, and betrayals as Aoteru uses his intellect to influence royal courts and generals, aiming to end the pointless bloodshed without relying on violence. The story adapts the structure of the classic Chinese novel Romance of the Three Kingdoms to a post-apocalyptic Japanese setting, bringing ancient military strategies to life amidst the ruins of a modern nation.