Pinoko and Sharaku are playing in a park when a stray dog grabs Pinoko's purse and runs off. They chase after the stray, but the dog is suddenly hit by a car outside of the park. Pinoko gets Black Jack to operate on the dog, and is successful.
A victim of a hit-and-run is discovered by a truck driver, Toru, and carried to Black Jack's house. The doctor performs an operation to save her life, but when she wakes up, they realize she has amnesia.
Konomi is a beautiful surgeon who can amputate patients' limbs without hesitation. Thus, people spread rumors and call her the female Black Jack. Her boyfriend proposes to her, but hearing the bad rumors, requests that she quit her job.
Pinoko is walking Largo in a park when they come across a large and old zelkova tree. An old man, the tree's self-appointed keeper, has been taking care of it, saying that it had saved his life during the war.
Black Jack and Pinoko come across a model who collapses in front of them. The doctor realizes she has cirrhosis of the liver, and starts operating on her after determining that the ambulance won't come in time.
A man appears at Tokyo Station and leaves a bag on the platform. He detonates a bomb in the bag, and emergency services come in the aftermath. Black Jack happens to be in the station and gives first aid to the victims.
Black Jack runs into a blind acupuncturist, Biwamaru, who has a keen nose and goes around healing people with his needles. He has even treated some of Black Jack's patients, and the doctor warns the acupuncturist to not approach his patients anymore.
The president of a printing company, Eizo, wants to hire Black Jack to play the part of his son. The doctor declines, but Eizo explains that only his son is acceptable to his older brother Eiichi to perform surgery on him.
Black Jack reminisces about his high school days, when he was known as Kuro Hazama. His classmate Gera loved to laugh, and Kuro tried to find out why. He didn't understand how he could laugh, especially after finding out Gera's parents abandoned him.
Black Jack arrives at a laboratory set up on the savanna. Dr. Togakushi had invited him there to help with research into a mysterious illness that is making animals and now people shrink and eventually die.
A doctor, Futoppara, who graduated from the same medical school as Black Jack now heads his own hospital. He is arrogant, and dismisses another young doctor's opinion that perhaps a certain patient was misdiagnosed.
A movie director, Tenma, announces at an awards ceremony that his next film will help save lives. Later, Tenma visits Black Jack and explains that he wants to film the doctor performing surgery on a patient with collagen disease.
A traffic cop, Kotaro, begins talking to a statue in the likeness of a police officer, opening up in ways he can't with actual people. He soon becomes obsessed with the statue and starts taking care of it, such as cleaning off graffiti.
Sharaku, his sister, Black Jack, and Pinoko are on an overseas trip visiting an archaeological dig headed by Sharaku's father. That night, a glowing staff that was recovered from the dig site guides a seemingly possessed Sharaku deep into the jungle.