Dr. Jotaro Honma is a pivotal figure in the life of the protagonist, known for being the skilled surgeon who saved a young Black Jack’s life following the explosion that killed his mother. Before this event, he was a famous and talented surgeon whose career was derailed by professional jealousy and skepticism regarding his research, leading to his expulsion from the mainstream medical community. He is visually distinctive, often depicted as a short, elderly man with a large, bumpy nose and white whiskers, and is consistently seen in his surgical attire. A recurring nickname for him is "Doctor Saruta," a persona that connects him to other works by the same creator, where he often represents a figure who profoundly understands the cycles of life and death.

Personality-wise, Dr. Honma is characterized by an unwavering kindness and a determined spirit. He is a compassionate man who believes in fighting for a patient's survival against any odds, a philosophy that deeply inspired the young Black Jack to pursue a career in medicine. Despite this heroic act, he was not without flaw; during the life-saving operation on the young Black Jack, he accidentally left a surgical scalpel inside the patient’s body. This mistake haunted him for years, a burden of guilt he carried quietly. His motivations are rooted in the purest ideals of a healer, emphasizing the power of nature and the inevitability of death, lessons he frequently imparts to his pupil. In the narrative of Black Jack 21, his role expands beyond that of a mentor, as it is revealed he was once involved with a secretive and large-scale project known as the Noir Project, linking him directly to the central conspiracy that Black Jack investigates.

His most significant relationship is undoubtedly with Black Jack, for whom he served as the principal father figure after the tragedy. This bond is complex, built on immense gratitude and inspiration but also shadowed by the secret of the forgotten scalpel. In a poignant turn of events, an elderly and ill Dr. Honma summoned Black Jack to his side, finally confessing his past mistake by presenting the very scalpel he had left behind, which his patient's body had safely encased in calcium. Shortly after this confession, he lost consciousness. In a final act of devotion, Black Jack attempted to repay his debt by operating on his dying mentor, but the procedure was unsuccessful, and Dr. Honma passed away due to complications of old age. His legacy endures beyond his death; a cure for a deadly virus is named the Honma Antiserum in his honor, and he appears in spirit among the figures who guide Black Jack during a critical moment of crisis.

As a surgeon, Dr. Honma possessed remarkable abilities, famed for his skill with a scalpel and his capacity to perform surgeries that other doctors deemed impossible, such as the reconstruction of the young Black Jack. His true legacy, however, lies in his role as a philosophical guide. More than any other character, he serves as the moral compass who reminds the often-defiant Black Jack of the natural order, the limits of medical intervention, and the importance of accepting death as an intrinsic part of life.