In Mutation, Cook again blends issues from the front page into a suspenseful scenario that draws out the ethical ambiguities of modern medical research. Dr. Victor Frank is an obstetrician-gynecologist who owns Chimera, a company doing bio-molecular research. When he and his wife, Marsha, turn to invitro fertilization to conceive their second child, Frank uses his skills to fuse animal genes into his own offspring and to create a child with exceptional genius. He then secretly applies this technology to two other invitro cases at his lab. When the originally healthy babies begin to die as young children, he starts to worry over the health of his own son, VJ. Meanwhile, he also tries to cope with a lawsuit by a female employee and an attempted takeover of the company by his partner.

Preoccupied by his work and proud of his handiwork, Frank is blind to VJ's increasingly secretive and atypical behavior. By the time he understands what his genetically altered son is doing, it is too late to control his behavior. Dr. Frank realizes he must destroy VJ to protect Marsha and society.

VJ (Victor Frank, Jr.) is a child genius. By the age of two he is sufficiently crafty to know that his exceptionality brings him too much attention; he therefore fakes a drop in intelligence to that of high normal. By age ten he is leading a double life — as a bright but shy child who shuns other children, and as a biological researcher and founder of his own biotechnology company. Sneaking into his father's lab, he steals the zygotes his parents have stored and manipulates their genetic structure so that he will have no competition from his now retarded brothers and sisters, who he begins to raise in an artificial womb. To obtain the lab equipment he needs, he blackmails employees in his father's company, who are embezzling funds, and later manufactures cocaine to raise cash to expand his research. When his older brother and nanny stumble upon his secret life, he injects them with a cancer-causing substance to eliminate them so he can continue his work. In the end, his father confronts him in the laboratory in an attempt to rid the world of the amoral monster he has created.

Dr. Marsha Frank, child psychiatrist and mother of VJ, becomes increasingly concerned about her son's lack of friends and disdain for affection. Her innocent attempts to improve the boy's social life lead her slowly to the knowledge that something is seriously wrong, and finally to the understanding that her son has murdered his own brother and nanny. Toward the end of the novel, she discovers that her husband has created a second child genius, and she must decide its fate.