A psychiatrist, Dr. Shaw, is called to the emergency room of a Goa hospital, where a highly agitated man is being held in custody. Dr. Shaw agrees to listen to his story. The man identifies himself as a doctor, and recounts, in flashback, the events leading up to his arrest and arrival at the hospital.
In the nearby town of Anjuna Dr. Peter Braganza sees a number of patients apparently suffering from Capgras delusion, the belief that their relatives have somehow been replaced with identical-looking impostors.
Returning from a trip, Peter meets his former girlfriend, Maria Gomes, who has recently come back to town after a divorce. Maria's cousin Veronica expresses the same fear about her Uncle John, with whom she lives. Psychiatrist Dr. Daniel Paul assures Peter that these cases are merely an "epidemic of mass hysteria"
That evening, Peter and Maria are urgently called to the home of Peter's friend, Jack Barbosa, who has found what appears to be a dead body in his home. Inexplicably, the body has no discernible facial features or fingerprints but, to their horror, within a short period of time it begins to take on the exact physical features of Barbosa. Later, another body is found in Maria's basement that is her exact duplicate. When Peter calls Dr. Paul to the scene, the bodies have mysteriously disappeared, and Paul tells Peter that he is falling for the same hysteria.
The following night, Peter, Maria, Jack, and Jack's wife Susan again find duplicates of themselves, emerging from giant seed pods in Peter's greenhouse. They conclude that the townspeople are being replaced while asleep with exact physical copies. Peter tries to make a call to the cops for help, but the phone networks are all jammed and the call can't be put through, so Jack and Susan drive off to seek help in the next town. Peter and Maria soon realize that all of the town's inhabitants have been replaced and are devoid of any sort of humanity. They hide at Peter's office for the night, vowing to stay awake so as not to be replaced by their duplicates.
The next morning, Peter and Maria watch from the office window as truckloads of the giant pods arrive in the town center. They listen as Sandeep Patil (the commissioner of police) directs the others to take them to neighboring towns to be planted and used to replace their populations. Paul and Susan, both of whom are now also "pod people", arrive at Peter's office with new pods for Maria and Peter. They reveal that an extraterrestrial life form is responsible for the invasion and that the pods, capable of replicating any life form, traveled through space and landed in a field. After their takeover, Paul explains, humanity will lose all emotions and sense of individuality, creating a simplistic, stress-free, superior world.
After scuffling with and knocking out the aliens (Paul, Susan, and Patil), Peter and Maria escape from the office. Outside, they pretend to be emotionless pod people but Maria screams when she sees a dog dart out into traffic, her reaction exposing their humanity. A town alarm is sounded and the couple flee on foot, pursued by a mob of pod people.
Exhausted, they manage to escape and hide in an abandoned Factory outside town, struggling to stay awake so their bodies won't be taken over. Later, they hear music, and Peter leaves Maria briefly to investigate. Over a hill, he sees a large greenhouse farm with hundreds of giant seed pods being loaded onto trucks. Peter returns to tell Maria, and upon kissing her, he realizes, to his horror, that she fell asleep before he returned and is now one of them. Maria sounds the alarm as Bennell runs away. He is again chased by the mob, and eventually finds himself on a crowded highway. After seeing a transport truck bound for other parts of the city and the state filled with the pods, he frantically screams at the passing motorists, "They're here already! You're next! You're next!"
Peter is now finishing his story back at the hospital. Dr.Shaw and the on-duty doctor step outside the room, the latter expressing his certainty that Peter is psychotic. Just then, a truck driver is wheeled into the hall on a stretcher after having been badly injured in an accident. The orderly tells the doctors that the man had to be dug out from under a load of giant pods coming from Anjuna. Now finally believing Peter's story, Dr. Shaw calls for the police to block the roads in and out of Santa Mira while he alerts the CBI
