Dr. Kenzo Tenma, a leading neurosurgeon at the Dusseldorf Hospital has received massive acclaim for his successful surgery on a famous opera singer. However, he is burdened by guilt. Due to pressure from the director, he had operated on the opera singer on the night that he was supposed to operate on another man. As a result, when the director’s orders him to operate on the mayor, he decides to ignore the order and instead works on saving the life of a young boy, brought to the hospital from the scene of a serial homicide. However, the boy's twin sister, who was brought in with the boy, and who still suffers from shock, keeps repeating the words 'kill him'.

The price for disobeying Dr. Heinemann's orders to operate on the mayor is costly for Dr. Tenma. His career begins to plummet. The boy whom he saved finally awakens, but a horrible incident occurs soon after.

Things look brighter for Dr. Tenma, now that Dr. Heinemann is dead. His career takes off, and even Eva tries to win him back. But unfortunately, all that success has drawn the attention of Detective Lunge.

Eva tries to threaten Dr. Tenma, unless he gets back with her, she would reveal to the police that the tie that was found at the scene of the crime is his!

Inspector Lunge investigates the murder of a prostitute and suspects a senator named Dr. Boltzmann of involvement. His dedication to his work however takes a toll on his family life. Meanwhile, the vindictive Eva continues to press Lunge to catch Tenma. She also has a new lover, her gardener.

Eva Heinemann is arrested for public drunkenness and hooks up with Roberto, with whom she was with the night before her arrest. Roberto then reveals his link to Johan and Eva confesses that she was actually a witness the night Junkers was killed by Johan.

In exchange for her life, Roberto tells Eva to confront Tenma, who is currently treating a mob boss at a country house. Eva is promptly wounded by Roberto when she is unable to complete her task but is saved by Tenma.

Schubert, with the help of Reichwein, re-explores his past with Karl Neumann's real mother and realizes his link to Johan. As news of Tenma's arrest spreads, various people react with shock and horror, with the exception of Eva Heinemann, who is insistent that Tenma pay dearly for rejecting her. Suk tries to leave the hospital he is in to try to help Tenma, but is stopped by the Prague Police who inform him that Grimmer has sent a note to them exonerating Suk from any involvement of the deaths of the police officers. Runge also gets news of the arrest as well, but he is more interested in the Mansion of Red Roses, where he obtains a letter possibly addressed to the twins' mother. Tenma is deported back to Dusseldorf.

Former patients of Eisler Memorial Hospital enlist the aid of Alfred Baul, a lawyer, to represent Tenma. Baul in turn asks for the assistance of Fritz Vardemann. Vardemann visits Tenma in prison, and agrees to take on the defense, but is then called to the hospital when his wife goes into labor with their first child. When Baul visits Tenma in prison, Tenma is shocked to see that Baul is Roberto. Roberto then says that Eva Heinemann will be his next target.

After hearing Roberto's threat against Eva, Tenma decides to confess to all charges against him so he can be placed in the same van transporting a prisoner to a Federal Penetentary as the prisoner is arranging for a jailbreak.

Tenma and Milch are on the run with the injured Gustav and Helene. Eva finds her life in danger when she discovers that the attorney she's supposed to meet, Mr.Baul, is none other than Roberto.

Martin, a hired hand, is hired by General Wolf's ex-associates to ‘take care’ of Eva. But his emotions get in the way of his orders.

Tenma manages to find Martin. A drunken Eva spots Johan at a party. Martin receives his final orders from his boss but his feelings gets in the way. And Martin gets way over his head when he tries to investigate Johan and his disciple, and the truth about his past is revealed.

Martin’s attempt to save Eva costs him his life, his last minutes with Tenma reveals a terrible secrets about Martin’s boss, Peter Chapek and the about the experiments.

Capek tries to berate Johan for his actions and tells him that everything should be done according to Capek's plans but Johan simply disagrees and disappears. Capek realizes his hold on his organization is crumbling and has his men pick up Nina in Frankfurt. Eva accosts the young man who was introduced to Johan, Christof Sievernich, demanding answers.

Capek reveals to Nina that her and her twin brother Johan are the products of a eugenics experiment designed to breed "the perfect children". Tenma has wounded Christof and is driving him and Eva to the hospital while demanding answers on Petr Capek. While Eva makes a phone call at a payphone, Tenma sneaks away.

As time passes, more people in Ruhenheim are being shot dead by mysterious people and each other. Both Grimmer and Lunge determine that the owner of a local hotel is Klaus Poppe, also known as Franz Bonaparta. After subduing a man who was giving weapons to everyone in the town, they obtain information that one of the ringleaders is in a second hotel.

It has been some time since the tragic blood battle, and everyone is working hard to put their lives back to normal. Tenma finally locates a woman he has been searching for, and she reveals some startling information.