Mugensai, also known as Master Shoin, is a mysterious masked individual who functions as both a supporting character and antagonist in the narrative's first season. He has long, silvery-grey hair flowing to his stomach and wears a distinctive hexagonal mask covering his eyes while leaving the lower face exposed. The mask is black, adorned with a white hexagon and a black circle over the left eye. His clothing consists of a white kimono, with his neck, chest, and arms wrapped in white bandages.

He wields a device called the Chronometer, capable of manipulating time. During a confrontation with Shinsaku, the Chronometer was severed in two by a katana. Mugensai is deceased by the time of the subsequent story, Bakumatsu: Crisis, where his gravestone appears.

Another figure later emerges, identifying as Mugensai the Second and claiming to have inherited the original's will and objectives. This successor asserts that the first Mugensai ultimately betrayed their cause. Mugensai the Second wears a light-colored shoulder cloak reminiscent of the Shinsengumi, a white jacket and trouser uniform, black gloves and boots, and has long dark blue hair. His most notable feature is a hexagonal eye mask accompanied by a wooden teeth open-mouth grin.

Mugensai the Second commands the Shinsengumi to locate the resurrected Chronometer, declaring his aim to forge a powerful nation of warriors that will resist foreign influence. He is resolved to secure the device and remove any opposition. This individual displays considerable power, having once shattered the swords of attacking Shinsengumi members without injuring them, and he can sense the Chronometer's presence. He is also responsible for ordering repairs on Susanoo Castle and is knowledgeable about large-scale space-time rifts.

The original Mugensai was the teacher of Takasugi Shinsaku and Katsura Kogoro. The dynamic between these disciples and their master is central to the consequences of altered history and the corrupting nature of power.