In New York City, a gunman perched atop a water tower opens fire with a .22 caliber rifle on the crowded streets below, randomly killing fifteen pedestrians. Peter Nicholas (Tony Lo Bianco), a devout Catholic NYPD detective, climbs the tower to talk to the sniper. Before jumping to his death, the gunman tells Nicholas that God told him to commit the murders.
Although traumatized by the attack, Nicholas investigates a series of seemingly unpremeditated murders that follow: a mass stabbing at a supermarket, a mass shooting by a police officer at a St. Patrick's Day parade, and a man who murders his wife and children. They have all been committed by a variety of unconnected, seemingly normal assailants who claim that God told them to kill. Nicholas learns that one of the murderers knew a long-haired young man named Bernard Phillips. When Nicholas visits Phillips' address, Phillips' mother assaults Nicholas with a knife, but she dies during the attack by falling down a flight of stairs. She turns out to have been a virgin and to have once claimed she was abducted by aliens. Nicholas' superiors refuse to acknowledge a religious motivation for the murders and suspend him, so he leaks this story to the press, causing a panic.
A group of men, members of a religious cult, are aware that their leader, Bernard Phillips (Richard Lynch), is influencing the murderers as he contacts and controls them via psychic powers and as he has informed them of each impending atrocity. Phillips has one of the members invite Nicholas to join them, but when Nicholas asks whether the follower knows about Phillips' mother, the follower suffers convulsions and drops dead. Another cult member attempts to kill Nicholas by pushing him in front of a subway train, but when he fails, Nicholas forces him to take him to Phillips, who isolates himself in a fiery furnace room deep underground. After delivering Nicholas, the follower decapitates himself using an elevator. A brief meeting convinces Nicholas that he himself is special and that Phillips does not kill him as he needs him for some purpose.
By researching his own adoption records, Nicholas finds an old woman who seems to be his birth mother. She explains that she gave up her out-of-wedlock child after she was brutally impregnated by a strange ball of light while she walked home from the New York Worlds Fair in 1941. The meeting distresses both of them, and Nicholas is wracked with doubt over who or what he is.
He confronts Phillips one last time and discovers the truth: both he and Phillips are the result of "virgin births" caused by a mysterious extraterrestrial "entity of light" with psychic/supernatural powers and advanced spacecraft technology. Nicholas' human genes are dominant, which is why he is unaware of his true nature, while Phillips is more like their unseen progenitor. Phillips reveals himself to be a hermaphrodite who wishes to spawn a new species with his "brother." Nicholas refuses and attacks Phillips, who uses his powers to destroy the building they are in and thereby commit suicide. Nicholas is arrested for the murder of Phillips. As he is led into court by police, a news reporter asks him why he committed the crime. He responds, "God told me to." Nicholas is committed to the Matteawan State Hospital for the Criminally Insane.
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