Three years after the decisive battle that ended Yamato Takeru, peace returns to the land. Takeru, Oto, and their friends settle back into village life, enjoying a period of calm. But one night the Shuranoo, piloted by Mikazuchi, reappears and attacks the village, wreaking havoc. Faced with no other choice, Takeru is forced to reactivate the sealed Susanoo from his slumber. Yet this is only the beginning of a new threat; Takeru must confront his own limits in order to rescue Oto from the looming danger.