The Emperor retains the formal title of ruler following the government's overthrow by the deity Susanoo, who seized control of Kyoto. Susanoo's new regime fundamentally reshaped the city's landscape and society, replacing the old political order with his divine authority. While the Emperor's position remains recognized, genuine power rests entirely with Susanoo and the forces upholding the altered timeline.

Arriving in Kyoto, Takasugi Shinsaku and Katsura Kogorou encounter this transformed reality and discover the Emperor's government deposed. Their mission pivots to resetting time, aiming to restore the original historical trajectory and return legitimate authority to the Emperor by destroying or controlling the time-manipulating artifact Susanoo exploited. This artifact, central to Susanoo's usurpation and the timeline alteration, becomes the focal point of the conflict. Resetting time is essential to undo Susanoo's rule and reinstate the Emperor's proper place within history.

The Emperor's role connects intrinsically to the broader resistance against Susanoo's imposed order. Though specific actions or policies are not detailed, the efforts of figures like Takasugi and Katsura to "save their nation" inherently involve restoring the Emperor's position against the illegitimate deity's rule. The struggle against Susanoo's forces defines this period, with the Emperor symbolizing the rightful order that requires reinstatement.