Chapter 1: Needle
After a man has surgery performed on him by Black Jack, a needle gets stuck in his vein due to an earthquake snapping his IV and causing the missing needle to go into his vein. Black Jack performs a second surgery to remove the needle but the needle disappears from the radar. Black Jack is forced to give up but finds out that the needle managed to find its way out of the man's arm and he is alive. Though relieved, Black Jack is frustrated he could not save the man himself and remembers Honma's words not to underestimate the human body.
Chapter 2: Granny
An old woman is driven out of her son's home as she continually asks for money. It is revealed when her son was young that she had a doctor heal him in exchange for 30 million yen. She paid for it over the years including working herself to death at night and selling her belongings. This same woman is slowly dying from a disease and Black Jack agrees to perform the surgery only if the son agrees to pay 30 million. Realizing all that his mother has done for him, he agrees.
Chapter 3: The Ballad of the Killer Whale
Black Jack recalls having treated a whale he named Triton who would frequently get himself injured by fighting with sailors and would bring payment to Black Jack in the form of pearls. While he befriended Black Jack, Black Jack grew to realize it was too dangerous for him to stay and begged Triton to leave. Triton would come with worse injuries but Black Jack refused to treat him and eventually Triton died.
Chapter 4: To Each his Own
A young man contemplates suicide after failing his medical college entrance exams until an older construction worker spends the day with him and convince him to live anew. That same worker gets into a severe construction accident and Black Jack does the surgery in exchange for the board dropping charges against him. The young man watches the surgery and his passion renewed, decides to become a doctor.
Chapter 5: Emergency Shelter
Black Jack goes to retrieve money from a crummy politician but he refuses to pay the 50 million yen. He instead suggests giving Black Jack a suite at his newly built disaster proof hotel. However, while testing it out, Black Jack, the politician, and the politician's potential buyers get trapped. The politicians promise to pay Black Jack handsomely if he frees them. However, when Black Jack manages to find the wire that connects to the power and frees them the politicians refuse to pay. Black Jack scolds them, saying money meant more to them than their lives.
Chapter 6: Dirtjacked
A teacher, a bus driver, and some elementary students are trapped in a cave in in a tunnel while driving alongside Black Jack. While the teacher protects the students, Black Jack takes a rich man's son among the group to get help and supplies. While he tends to the wounded, the teacher sacrifices herself to protect the children.
Chapter 7: Where Art Thou, Friend?
A flashback as to how Black Jack received his skin. No one wanted to donate skin except his african friend Takashi and looks back at how he went through three years of intense rehabilitation. He then searched for his friend for years and received a letter saying he has become a doctor for the Earth. Later, Black Jack soon sees news of how his friend, who became part of an environmental group, died during a protest. Black Jack then states his skin has now become a memento.
Chapter 8: Kidnapping
A hitman kidnaps Pinoko to coerce him since Black Jack is set to do an operation on a good President who they wish dead. Black Jack pretends to have failed though it is revealed he faked the President's death and the two manage to escape and have the assailants arrested.
Chapter 9: Assembly Line care
A doctor operates his hospital like an assembly giving little proper care for patients. His patients start leaving and he blames Black Jack for giving his hospital a bad name but when his daughter's life is in danger, he realizes his mistake.
Chapter 10: Helping Each Other
A young man vouches for Black Jack when he goes under suspicion of theft. Black Jack returns the favor when the man's company wish to use him to save their reputaiton due to a scandal between the president and prime minister at the expense of his life. Black Jack performs surgery on him and then plastic surgery to change his face to escape his cruel company.
Chapter 11: Stradivarius
Black Jack and some passengers are forced to make an emergecny landig du to extreme cold. A violinst loses his violin while the group travels to a remote village and continues to go into the snow to find it. He endures frost bite and without his tools, Black Jack is forced to amputate his fingers.
Chapter 12: Pinoko's Challenge
Pinoko tries to apply for high school but the stress of the test proves too much for her body.
Chapter 13: Hospital Jack
While operating on a child patient, the hospital black jack is in is under hostage by some terrorists in exchange for monetary compensation from the government. The situation boils over and the hospital loses power but Black Jack manages to perform the surgery in the dark.
Chapter 14: Blind Acupuncturist
A character from another of Osamu Tezuka's works treats people for free using accupuncture, much to Black Jack's distress. However, Biwamaru, the blind acupuncturist, inadvertedly makes a patient's condition worse due to her fear of needles and Black Jack operates. As thanks, Biwamaru uses acupuncture to fix Black Jack's weak organs.