The film is set several years after the events of the first two films. It begins with a woman going into labor in a cab on a rainy night. Panicked, the cab driver seeks out a police officer to assist in the birth before going to search for a public phone to call for an ambulance. While he is away, the woman gives birth to a mutant baby. Recognizing it as a mutant baby like the ones from the first two films, the officer tries to shoot and kill the baby, who instantly reacts by killing both the officer and its mother. The following day the mutant baby's corpse is found inside of a Roman Catholic church where it had dragged itself to die.The film then cuts to a courtroom, where Stephen Jarvis (Michael Moriarty) is pleading for the court to spare the life of his mutant baby son, who he argues is acting aggressively because it is reacting to the hostility of the people and the chaos that is surrounding him. The baby breaks out of the cage that it is locked up in but is soothed by Jarvis, which convinces the judge to spare the baby and four others like him by quarantining them on a remote deserted island.After the trial, Jarvis is treated like a social pariah, as he is unable to work his former acting job and the child's mother, Ellen (Karen Black), only wants to live her own life without him, as if she had never even given birth in the first place. This eventually leads to Jarvis becoming extremely bitter, as he is unable to pay his legal fees and women want nothing to do with him, afraid that he will even pass along the mutation through casual touch. Meanwhile, fully aware that the five mutant babies are still alive and that their mutations were a side effect of a drug that his pharmaceutical company had produced, Cabot (William Watson) and some of his associates travel to the island in order to kill the mutant babies so that the company can make the same drug under a new label, only for the entire party to get killed and eaten by them.Five years later...Jarvis is approached by Lieutenant Perkins (James Dixon), who tells him that he has been recruited by Dr. Swenson (Art Lund) to launch an expedition to the island to study the mutant babies' growth and that he wants Jarvis to accompany them. Unfortunately, this expedition also turns out to be a disaster, as only Jarvis and Perkins are left alive - Perkins has been left deserted on the island while Jarvis remains on the boat as the mutants' captive, as they want to travel to Cape Vale, Florida. While traveling Jarvis realizes that the babies have both matured quickly and become adults, as one of them has given birth to a mutant baby of her own. It is implied, but never actually stated out loud, that Jarvis' son is the father of this mutant baby. Jarvis also realizes that the mutants communicate with each other through telepathy and that the only reason he is still alive is because of the existence of the dead bodies of the ship's crew and because his son has been protecting him all this time from the other mutants. He also realizes that the children are traveling to Florida in order to find Ellen. Eventually their ship comes across another one, at which point Jarvis' son throws his father overboard in order to save his life, fully expecting that this ship will pick him up.When Jarvis wakes up he finds out that he is being held captive in Cuba, but manages to convince his captors of his identity and that the mutant children pose a danger to all those around them. He also manages to convince them to take him back home. Meanwhile, the mutant children have already arrived in the United States, where they promptly kill several people who even so much as appear to be a threat to either themselves or Ellen, while also defending the life of a woman who is being attacked by a gang of punks. Ultimately both Jarvis and the mutants find Ellen, after which the mutants try to get her to take their baby. At first reluctant to do so, Ellen finally takes the mutant baby after Jarvis convinces her that its parents looked for her both out of love for their baby, as they were both already dying of measles and would ultimately be unable to care for it, and because they strongly and instinctively associated Ellen with motherhood. Jarvis and Ellen both accept the mutant baby as their own just as its parents both die of measles, while the final remaining adult mutant distracts the police, allowing the two of them to escape with the baby. The film ends with the two of them driving away together with their new mutant baby in search of a safe place to raise it.