Born Miyagawa Katsugorō in 1834 to a Musashi Province farming family, Isami Kondō was adopted by Tennen Rishin-ryū's third master, Kondō Shūsuke. He assumed the name Kondō Isami upon becoming the style's fourth head in 1861, taking charge of Edo's Shieikan dojo. His 1860 marriage to Matsui Tsune connected him to the Shimizu-Tokugawa clan via her father's retainer status. He fathered a daughter, Tama, in 1862, and later an illegitimate daughter, Oyu, with a Kyoto geisha during his Shinsengumi service.
Kondō co-founded the Shinsengumi in 1863, evolving from the Rōshigumi and Mibu Rōshigumi alongside figures like Hijikata Toshizō. As commander, he led with warmth and charisma, fostering deep loyalty and treating his men as family. He extended kindness and protection even to outsiders like Chizuru Yukimura, aiding her search for her father despite security risks. His trusting nature valued redemption and saw potential good in others, sometimes prompting Hijikata's cautions against naïveté. Kondō possessed a strong moral compass, reacting with horror to breaches of etiquette or unintended harm to allies. Despite his approachability, he demonstrated combat resolve, personally leading critical operations like the 1864 Ikedaya Inn raid.
His leadership faced severe tests, including the assassination of former ally Itō Kashitarō over political differences. Kondō lured Itō into a trap with drinks preceding an ambush, an act that triggered a revenge attack leaving Kondō mortally wounded. After recovery, his ambition for social recognition intensified, especially following a promotion to hatamoto status in 1867. This drive led him to accept the high-risk mission to seize Kōfu Castle during the Boshin War. His insistence on fighting "as a man" against overwhelming odds caused disillusionment in key members like Nagakura Shinpachi and Harada Sanosuke, who abandoned the Shinsengumi. Witnessing a subordinate's death during the battle prompted Kondō to acknowledge his tactical error and order a retreat.
In the Shinsengumi's final days, Kondō prioritized his comrades' survival. Facing imperial encirclement in 1868, he overrode Hijikata's objections, invoking his commander's authority for the first time to act as a decoy and facilitate escape. He surrendered under the alias Okubo Yamato but was identified and captured. After imprisonment and trial, he was executed by beheading on May 17, 1868. His final acts included entrusting Chizuru with funds for her safety and urging her to protect Hijikata, whose transformation into a Rasetsu he regretted enabling.
Prequel media reveals earlier struggles, including financial hardship during the Shinsengumi's formation and tensions with co-commander Serizawa Kamo. An incident where Kondō's booking error at the Honjou Inn provoked Serizawa to arson forced Kondō to apologize on his knees. His protective instincts extended to Okita Sōji, whom he raised from childhood and personally searched for when Okita fled during the Rōshigumi period. Kondō was 29 during the Shinsengumi's peak activities in Kyoto.