Isami Kondō commands the Shinsengumi, an organization formed to uphold order in Kyoto during the Bakumatsu. Hailing from Edo, he co-founded the group and serves as its chief, embodying its moral compass. His leadership radiates warmth, compassion, and profound trust in others, frequently granting the benefit of the doubt—a trait his confidant Toshizō Hijikata observes can verge on naïveté. Despite this, Kondō exhibits formidable mental and physical resilience, accepting accountability for both his choices and his subordinates' actions. His charismatic, jovial demeanor fosters fierce loyalty among the Shinsengumi, who revere him as a father figure.

Kondō shares a lifelong bond with Hijikata, forged in their youth through shared dreams of becoming warriors despite non-samurai origins. He holds deep paternal affection for Souji Okita, whom he raised from childhood into a master swordsman. While frequently deferring to Hijikata's tactical expertise for crucial decisions, Kondō asserts his authority as commander when needed. His protective nature extends to Chizuru Yukimura, a girl seeking her missing father; he welcomes her into the Shinsengumi despite security risks, safeguards her well-being, offers emotional support, and champions her inclusion.

Kondō navigates turbulent political and personal trials. During the Shinsengumi's inception as the Rōshigumi, he forms a precarious alliance with the volatile Kamo Serizawa, leveraging Serizawa's political ties to secure official recognition from the Aizu Domain. This era demands Kondō temper Serizawa's recklessness while preserving the group's honor, sparking internal strife. Later, driven by faith in redemption, he invites ideological rival Itō Kashitarō into the Shinsengumi. Following Itō’s betrayal and assassination, Kondō suffers grave injuries in a retaliatory attack, necessitating prolonged recovery in Osaka.

As the Bakufu crumbles, Kondō accepts a hatamoto title and land from the shogunate, charging the Shinsengumi with securing Kōfu Castle. This ambition compels him to pursue victory at any cost, culminating in a catastrophic battle where he witnesses needless slaughter. Confronted by this tragedy, he acknowledges his strategic missteps, orders retreat, and attempts self-sacrifice to atone—only to be dissuaded by Chizuru. In the Shinsengumi’s final hours, Kondō volunteers as a decoy to enable his remaining members' escape. Overruling Hijikata’s protests with a final assertion of authority, he surrenders to enemies to ensure their survival. He is executed by beheading in captivity.

Kondō personifies steadfast idealism and devotion to the Shinsengumi’s ethos. He exclusively wears traditional Japanese garb, spurning Western uniforms to symbolize his allegiance to samurai values. His conviction in humanity's inherent goodness and his vision of a dignified future for his men define his leadership—even as external turmoil and personal ambitions precipitate tragic outcomes. His legacy endures through the loyalty he ignited and the sacrifices he made for the Shinsengumi’s endurance.