Dr. Kenzo Tenma is a young and talented neurosurgeon. Although he was born in Japan, he decided to conduct his surgical residency in Dusseldorf, Germany, in the hopes of being able to do advanced medical research. He is currently a rising star at Eisler Memorial Hospital, with many speculating that he will soon be promoted to Director of Surgery. Hospital Director Heinemann favors Dr. Tenma, having even arranged for him to marry his daughter, Eva.

After saving the life of a famous opera singer, Dr. Tenma is praised by his superiors for elevating the reputation of the hospital. However, shortly afterward, he is confronted by a grieving widow whose husband, a Turkish laborer, was skipped over regarding surgical priority in favor of the more high-profile opera singer. As a result, a less skilled doctor operated on her husband, who died on the operating table. This encounter shakes Dr. Tenma, who begins to question why he was ordered to operate on the opera singer when the Turkish man arrived at the hospital first and, therefore, should have been his patient.

Dr. Tenma's morals are further tested when a similar situation arises: Johan Liebert, a young boy, is brought to the hospital in critical condition, having sustained a gunshot to the head. His parents have just been murdered, and his twin sister, Anna, is physically unharmed but mentally traumatized. However, just as Dr. Tenma is set to operate on Johan, he is ordered instead to shift his priority to the mayor of Dusseldorf.

Dr. Tenma decides to defy Director Heinemann's orders and proceed with the surgery on Johan. He successfully saves the boy's life, but the mayor dies under the care of a different surgeon. Dr. Tenma is blamed for the mayor's death, and he is demoted. The director, who once favored him heavily, promises that he will now work to bar Dr. Tenma from advancing in the medical field in any way. His fiance, Eva, breaks up with him as well.

Dr. Tenma resigns himself to a career with no possibility of promotion. He firmly believes that he made the morally correct choice and condemns the greed and political influences that seem to drive many other doctors, even going so far as to wish them dead in a fit of anger.

Director Heinemann decides to stage a photo shoot of the Liebert twins being reunited to recover some of the hospital's reputation after the mayor's death. Dr. Tenma disapproves, but with his reputation tarnished, his concerns are overruled. He is further angered when the director informs him that he will no longer be responsible for Johan's care.

Soon after, Director Heinemann and two other high-ranking hospital officials are found dead, having all eaten poisoned candy. The Liebert twins also disappear. The local police are joined in their investigation by Inspector Lunge from the Bundeskriminalamt (BKA), the Federal German police force. Since Anna and Johan's parents were refugees from Soviet-controlled East Germany, the investigators speculate that the crimes may have been politically motivated. Lunge, however, is suspicious of Dr. Tenma, viewing his recent fall from favor as a potential motive for wanting the director and the other hospital officials dead.

As a result of the deaths of three of his superiors, Dr. Tenma is named the Director of Surgery, and his reputation is restored. Over the next nine years, he continues to operate under the principle that all lives are precious and should be treated equally.

Meanwhile, the investigations into the Liebert murders, the hospital official murders, and the twins' disappearance stagnate. Inspector Lunge is now tracking a possible serial murderer targeting...