Makoto Tsukishiro serves as an executioner for the Tokugawa shogunate's secret police, Nue, in an alternate 1931 Japan. Publicly, Makoto maintains a cover identity as a bandoneon performer, projecting a soft-spoken and educated facade. This masks a deceptive and manipulative core, where Makoto readily employs lies to achieve objectives, viewing the world through a lens of pessimistic determinism where everyone is confined to roles.

Privately, Makoto specializes in intelligence gathering for Nue and wields athletic combat prowess, employing weapons such as a heated cane sword and glass grenades disguised as fragrance bottles. A significant detail involves Makoto binding their chest, revealed when Nue leader Jin Kuzuhara slices open Makoto's shirt during an interrogation regarding potential treason. Makoto expresses disgust during this exposure. The character demonstrates complex relationships with fellow executioners, notably displaying possessiveness and potential romantic feelings toward Sawa Yukimura. This culminates in manipulating Sawa's adoptive sister, Asahi Nakamura, by supplying poison pills intended for Sawa—an action Makoto attributes to emotions interfering with judgment. Despite these conflicts, Makoto persists in Nue missions, including operations against targets linked to the insurgent group Kuchinawa.

Makoto's narrative involves suspicions of treachery within Nue, particularly when Jin confronts Makoto over informant deaths following a stolen agent roster. Makoto initially deflects suspicion onto Sawa. Later, Makoto advises Sawa to separate from Asahi for protection, indirectly influencing Sawa's decision to send Asahi to a temple.