It's been years after the events in the first and second movie and the American public are well aware of the muntant babies. There is a trial going on, about what to do about them, and prosecutors want them exterminated while the defense attorney Stephen Jarvis (Michael Moriarty) wants them to be let to live.
It is revealed that one of the babies is his son, whom the prosecutor brings out. The intention was that it would either attack Jarvis or make him revolt his own flesh and blood. It fails to do either but the baby breaks out of its cage and hops onto the Judges table. Jarvis manages to calm his son down while at the same time advises the judge not to show any fear, and surprisingly it works. It is then decided that the babies were to be sent to a remote island so they won't harm anyone else; at the same time the parents are relieved that their children won't die.
Four years later Jarvis quits his job and works as a shoe clerk, he is met by an older lieutenant Perkins (James Dixon) who tells him that he has a chance to see his son on an expedition lead by them and a few scientists, to check on the babies. They go to the island and the babies, now fully grown attack and kill the scientists, Jarvis is left alive and Perkins is left on the island. All the fully grown mutants are stowed away and living off the dead scientists, and crew members for sustenance. Jarvis is the only survivor because the alpha male of the group is his son. They reveal to Jarvis that they are headed for the Florida keys and throw him off the boat in a life raft. Although he is alive he is rescued/arrested by Cuban authorities that think he is an American spy.
Meanwhile the mutants are looking for Ellen Jarvis (Karen Black), killing those in their way or whom have tried to harm her. Many of the mutants are hunted down and killed by the police but Stephen's son and another have tracked Ellen down. Stephen makes it just in time to tell Ellen that it is her son.
It is revealed to them that the mutant hanging around with the Jarvis mutant, is his mate and they have a child. They were slowly dying of the measles that they would have been treated for had they not been left on the island. They give the child away to Stephen and Ellen who recognizes them as its grandparents.
After all the mutants are dead, the Jarvis family sneek their grandson out in hopes to raise him alone in peace.