A poacher traps an endangered Iriomote cat on a remote island and boards a ferry. On board is Black Jack and Pinoko, along with a haughty politician. The wild cat escapes, causing a ruckus, and injuring the politician and a passenger's baby. The politician tries to get treated first by offering money, but Black Jack begins by operating on the Iriomote cat.

Sharaku is a middle-schooler who is often bullied. One day, Pinoko saves him from Kong, a bully, and they become friends. Sharaku suddenly becomes gravely sick and Black Jack is called into the hospital to operate on him. However, a freak accident causes an IV needle to break off and be carried away in his vein.

At Tom, their favorite cafe, Black Jack and Pinoko encounter a boy with a physical disability who is intently reading a book by a handicapped person. Inspired by the memoir, and as a way to rehabilitate his legs, he decides to walk 350km from Hiroshima to Osaka, by himself.

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.

The bully Kong comes home to his sister Chako, who has been diagnosed with tuberculosis and another unknown disease. Chako, having heard about Black Jack, wants her brother to find him and take her case.

Doctors at Manaka Hospital hold a conference to decide the successor to the recently deceased hospital director. There are two veteran doctors with 20 years experience, however, one other doctor with similar experience is overlooked, Dr. Shiitake.

A boy is reluctant to go to school because he is afraid of his strict teacher, Mr. Muramasa. The teacher explains to this co-workers that he tries to motivate students by a tough-love approach.

Black Jack and Pinoko visit a zoo to see a white lion cub named Luna Luna, but the lion is sick. Pinoko and the lion's keeper beg Black Jack for help, but he refuses.

Black Jack takes Pinoko to his favorite sushi restaurant. The sushi chef, Taku, after years of training, feels that he is now ready to make the best sushi in Japan for his blind mother. However, while heading back to his mother's home, he is hit by a truck and loses his arms. The truck driver Akira is shocked to learn of the victim's predicament. The two later meet at the police station.

An old lady is forced to leave her son's hospital where she is living when it becomes full with patients. The son's wife proposes to have her sent to a nursing home, but the son refuses. Pinoko and Sharaku befriend her and offer a place to stay, but she politely declines.

Black Jack receives correspondence from overseas regarding a 200-year-old patient suffering from a painful disease. A relative of the patient offers 10 million dollars for successful treatment. Black Jack at first decides not to go, but later changes his mind. He and Pinoko fly out and is greeted by Miriam, the letter writer and relative of the patient.

Pinoko notices that Largo has fetched a pearl. She shows Black Jack, which surprises him, and he heads out to the shore. Pinoko and Largo follow, and they come across a bay filled with shining pearls. Black Jack tells Pinoko the story of the killer whale Triton. Five years before, Black Jack discovered the injured orca and treated him.

Pinoko and Sharaku watch a TV show, and Pinoko takes a liking to the monster villain of the show instead of the hero. Sharaku is friends with the show staff and Pinoko ends up visiting the set at the TV studio. She becomes a fan of the actor inside the monster suit, Takao. The staff notice the actor's badly swollen leg and ask Sharaku to introduce Black Jack.

Kazuo is a star gymnast at the local high school Everyone has high expectations that he will medal at the athletic competition, but he feels pain in his left arm. His classmate Toshie notices the swollen arm is getting worse, and alerts his mother. Kazuo is sent to a clinic where he is diagnosed with gangrene. Against the doctor's advice to rest, he continues to practice for the competition.

Pinoko visits a pool with Sharaku, and despite Black Jack's warning not to go into the water, she goes in with an inner tube. She begins to drown, but is saved by Musashi, a lifeguard who also works as an animator. They become friends, and she becomes interested in his animation work.

Michiru learns that she has terminal cancer and only a few weeks left to live. Her dying wish is to marry the next man who walks into her hospital room, even if it is just a token wedding.

Black Jack performs an operation to treat an aortic aneurysm. The four foreign doctors who watch the surgery are astonished with his technique. They are from the world medical federation, and upon finding out that Black Jack is unlicensed, decide to help him get a license from the Japan Medical Association.

Rei is the school's star vocalist, and is popular among the students. Kumiko notices Rei coughing in pain. However, she continues to sing, practicing for a contest coming up in three months. Rei asks Kumiko if her father, Dr. Honma, can examine her. Rei reveals that her father had passed away.

Jun has a best friend that he has never met before in person. He is Tom from New Zealand, with whom he chats often online. Although Jun's condition doesn't allow him to play sports, he tells Tom he plays baseball. Jun's mother disapproves of the charade, but he says that Tom will never find out. Jun's parents discover that Black Jack can treat him, albeit for a price.

Black Jack and Pinoko are on vacation in snowy Nagano. On the bus, they see a mother who is taking her daughter Tsuyuko to a village clinic. Suddenly, Pinoko has stomach pains, and she and Black Jack get off the bus with the mother and child to visit the Kowa Clinic.