Black Jack is a doctor who operates on a breed of superhumans which are able to excel at various activities like sports, arts and science. However they are prone to deteriorate over time. Joe Carol Brane hires Black Jack to find a way to stop this.
During his childhood, Black Jack was bullied due to his cruel appearance and an aloof attitude which made it difficult for him to make friends. However, he found an unlikely companion in Gerra Hazama who loved to laugh. One day goons from the mob came to his house and stabbed him in the neck, leaving him unable to laugh again. This inspired him to become a doctor so that he can bring happiness to people.
He gets a chance to do so when a wealthy businessman named Kagemitsu Hazama approaches him for the first time in 21 years. He offers money and a partnership in his crime syndicate in return for plastic surgery on his second wife who was burned in a fire. Black Jack agrees.
Before the operation begins, an autopsy is performed which reveals that the girl had a rare cancer called Teratoma–a twin cystic tumor that develops when one twin does not fully separate from the other. Black Jack tries to remove it but as he is about to cut the girl, a voice screams at him not to cut. She dies soon after.
Afterwards, Black Jack reflects on how Pinoko came into his life. One night some years ago a group of doctors visited him with a little girl who had this tumour. He agreed to operate but realised that the operation would only work for five minutes at most. He then realises that the tumour had multiplied to an unimaginable size and that it was now growing inside the girl’s internal organs causing them to age at an incredible rate.
Later, Black Jack and Pinoko meet a man with a caruncle covering half of his face. He explains that he has Dissociative Identity Disorder and has two personalities. The violent one emerges when he sees something frightening. Black Jack successfully removes the carbuncle and the personality but it returns after a while.
After visiting the damaged Sky hospital, Black Jack and Pinoko travel to a Middle Eastern town. While there, they befriend a man with an Arabic name who has a distorted face from a carbuncle. He tells them he has a violent personality which emerges when he is stressed. Black Jack removes the carbuncle and the personality again but it returns after a while. He then explains that he has a second personality which emerged when his fiance died.