The Federal Unites Air Force attacks the Ortega republic accusing its leader General Cruz of international criminal activities. Meanwhile, Black Jack is asked by a woman called Maria to operate on an unknown person. During transit, Ortega forces free Cruz, and Captain Maria Carnella is shot in the eye. She contacts Jack who says the patient is Cruz who is dying from cancer. On the perilous journey back to Ortega, Black Jack operates under moonlight to remove a cancerous lesion on Cruz's thyroid gland to prolong his life. Meanwhile, Federal Unites elite forces attack and the Ortega forces create a diversion, however they are defeated and Maria gives her life to save her father, General Cruz. Jack carries Cruz to the border, but he is killed under orders of Federal Unites President Kelly. Later, back home, Pinoko finds Maria Carnella's dog tags in a drawer.

Near the remote village of San Ferna in the Andes, an ancient beech tree is about to be cut down to make way for a highway, but old man Armando protests that it protects the village. Jack receives a telephone request from Andrew, a boy whose brother Lawrence has plants beginning to sprout from his body. Jack and Pinoko travel to the outskirts of London where he examines Lawrence, but finds no clinical explanation for the plant. That night Lawrence disappears and while Jack and Andrew search for him, he appears at Jack's hotel and takes Pinoko with him to the airport from where they fly to San Ferna. Jack and Andrew follow them and reach the boys' parents' house but Lawrence has not arrived. Meanwhile, Armando is camped near the ancient tree and he hears it tell him to find the children. Jack finally finds them, and after a thorough examination he finds that a seed from a beech tree, Fagus Sieboldii, has taken root within his body and is beginning to take control. Jack operates to remove the parasitic plant, and Lawrence begins to recover. On the day the ancient tree is to be felled, Lawrence arrives and sings to it. It flowers, then disperses its seeds before it withers and dies.

A street urchin attacks and damages luxury cars, and the case is handed to Takasugi in the Juvenile Division. Investigators find a match between the youth's fingerprints and a woman known as the Love Hotel Killer who has been killing her clients. Meanwhile, Jack is called to examine Koichiro Tsuzuki, the young head of the Tsuzuki corporation who has developed a large carbuncle-like tumor on his abdomen which resembles a human face. Some nights he mysteriously disappears for hours. Meanwhile, a beautiful woman calling herself Ryuko, seduces and kills men who cheat on their wives. Later, Jack encounters Mariko, a homeless teenager, who asks him to help her wounded friend Ryuko, whom he discovers has a carbuncle similar to that of Koichiro. When Jack returns to the Tsuzuki residence he finds Ryuko there and the carbuncle then changes her back into Koichiro. Jack determines that Koichiro suffers from a dissociative identity disorder and operates to remove the tumor, but during the operation, the personality of Jun, a street urchin surfaces and he escapes. Suddenly, the police arrive to arrest Koichiro Tsuzuki who has the same fingerprints as the urchin and serial killer on suspicion of the recent murders. Jun attacks the police and is shot, transforming back into Koichiro before dies.

The D.L. Chemical company is found guilty of poisoning people who ate fish caught in the bay which were affected by the toxic waste that flowed into Mikazuki Bay. It is ordered to pay damages for many people who have died and hundreds who have suffered various symptoms as a result of heavy metal toxemia. Representatives from D.L. Chemical ask Jack to assist in helping 300 patients urgently needing surgery. Jack and Pinoko stop at a Shinto shrine, which locals call the Mermaid Shrine. It based on the story of Jiro, a fisherman fell in love with Nagi, a mermaid. Nagi prayed the Lord of the Dragon Palace to change her tail into legs so she could be with Jiro, however when she dived back into the water to find a blue pearl demonstrate her love for Jiro, she drowned. Jack and Pinoko stay a Inn and hot springs where they meet Tsukiko, a young woman crippled by the Mikazuki syndrome who sells fish for a living even though the buyers don’t eat them. Jack visits Dr. Fox at the hospital to discuss to project, but rumors circulate of an unlicensed doctor on the team, and Jack declines to work on the project. Returning home, Jack sees Tsukiko who is no longer able to walk and he performs knee replacement surgery. However, Tsukiko misses the sea, and one night she returns to the bay and drowns. When carrying out the autopsy, blue pearls are found in her duodenum which Jack keeps as a possible key to curing the Mikazuki syndrome.