Several years after the events of the first two films, Ellen Jarvis, Karen Black, finds herself in a tense moment of chaos when a woman goes into labor in a cab on a rain-slick night. Panicked, the cab driver seeks help from a nearby police officer and scrambles to find a public phone to call an ambulance. While the driver is away, the woman gives birth to a mutant baby, and the newborn’s hostile reaction to danger leads it to kill both the officer and the mother. By the next day, the mutant baby’s corpse is discovered inside a Catholic church, where it has dragged itself to die.
In a courtroom, Stephen Jarvis, Michael Moriarty pleads for mercy, arguing that the child’s aggression stems from the harsh world around him. The baby breaks out of its cage, but Jarvis manages to calm it and convinces the judge, Judge Watson, Macdonald Carey, to spare the child and four others by quarantining them on a remote island. The verdict fractures Jarvis’s life: he becomes a social pariah, unable to work his former acting job, and Ellen, wanting a chance to live apart from him, seems determined to start anew. The root cause of the mutation traces back to a medication produced by Cabot’s pharmaceutical company, a connection exposed by Dr. Brewster, Neal Israel, who has been drawn into the corporate conspiracy.
Five years pass before a new turn arrives. Lt. Perkins, James Dixon approaches Jarvis with news that Dr. Swenson, Art Lund has recruited him to lead an expedition to the island to study the growing mutants. Jarvis joins the perilous voyage, but the mission quickly unravels: only Jarvis and Perkins survive, with Perkins being deserted on the island while Jarvis remains on the boat as the mutants’ captive, as the telepathic children press forward toward Cape Vale, Florida. Jarvis soon realizes the mutants have grown into adults and even birthed a new child, with the implication that his own son may be the father. The mutants communicate with each other through telepathic links, and Jarvis suspects that his survival hinges on the bodies of the sailing crew and, more importantly, on the protection offered by his unseen son.
Captured and transported back toward home, Jarvis awakens in Cuba and uses his wits to convince his captors of his identity and the danger the mutants pose, persuading them to take him back to the United States. Meanwhile, the mutant children have reached American shores, where they kill several people they see as threats to Ellen while also stepping in to defend a woman under assault by a gang of punks. The reunion with Ellen follows, and the mutants urge Ellen to care for their child. After a hesitant start, Ellen agrees to take the child, swayed by Jarvis’s insistence that the mutants’ actions come from a deep, parental love and their current inability to care for the infant due to measles and their fierce instinct to protect. With Ellen’s acceptance, the mutants die, and a final distraction by the last surviving adult mutant clears the way for Jarvis and Ellen to escape with the child. The movie closes as they drive away together, seeking a safe place to raise their unusual family.
