Isami Kondō commands the Shinsengumi, Kyoto's special police force during the Bakumatsu. His leadership reveals compassion when he permits Chizuru Yukimura to stay at headquarters after she witnesses a Fury attack, partly due to her connection to her sought-after father, Kodo Yukimura.

Within the group, Kondō holds authority and respect, mediating decisions and approving critical operations. He oversees the search for Kodo and manages internal strife, including the departure of members aligned with Kashitaro Itou. Strategically, he collaborates closely with Vice-Commander Toshizo Hijikata, sanctioning actions like placing Hajime Saito as a spy within Itou's faction to watch for treachery.

Kondō's leadership faces severe trials when Itou's followers attack him. Suffering gunshot wounds, this assault critically impacts the Shinsengumi. The severity of his injuries contributes to Okita Souji's desperate choice to consume the "Water of Life," transforming into a Rasetsu for vengeance.

Even amidst mounting pressure from factions like the Satsuma-Choshu alliance and betrayals such as that of the Yodo clan, Kondō's role remains central to the Shinsengumi's cohesion and objectives. His actions prioritize the group's stability and mission until his incapacitation.