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In New Mexico, policemen Ed Blackburn and Sgt. Ben Peterson find a little girl who is stunned and unresponsive, walking through the desert, tightly gripping her damaged doll. Nearby, they find an unoccupied trailer hitched to a car by the side of the road, its metal hull ripped from the inside out. While they investigate, they hear a high-pitched buzz and discover a large, unusual animal footprint on the ground. On their way back to town, the policemen find that a general store has been wrecked and its owner mysteriously killed. Ed stays behind to guard the store, and he, too, is brutally killed after hearing the high-pitched sound. Later, the coroner reports that the storekeeper died from a large injection of formic acid, not from the many fractures on his corpse. Upon learning that the owner of the trailer was a vacationing agent, the FBI sends Robert Graham to investigate. Bob sends a cast of the animal track to the FBI's Washington, D.C. headquarters, and in response, Department of Agriculture entomologists Dr. Harold Medford and his daughter and fellow scientist Patricia, are flown in. At the hospital, Harold examines the little girl, who remains traumatized and uncommunicative until he uncaps a bottle of formic acid under her nose. Jolted into a panic, she screams "Them! Them!" Although Harold has a frightening theory, he withholds it, until it is later confirmed by the appearance of a nine-foot, insect-like creature at the trailer site. By ordering his companions to shoot at the creature's antennae, Harold saves the group from its attack and the creature is killed. Harold then explains that it was a descendant of an ant that was present when the atomic bomb was first tested in the desert in 1945, mutated each generation by lingering radiation. With the help of the local Air Force officers, Brig. Gen. O'Brien and Maj. Kibbee, Harold instigates an aerial search of the desert for the creature's nest. When the nest is found, it is torched and its tunnels gassed with cyanide. Afterward, to determine if all the ants were killed, Bob, Ben and Pat gear up and enter the nest, rappelling through the tunnels hundreds of feet into the earth. After passing many gigantic, dead ants, they reach the queen ant's nest. Seeing that two eggs have hatched, Pat anxiously orders that everything be burned. Back on the surface, Harold and Pat announce that the problem is not over, as two queens appear to have hatched and escaped before the nest was destroyed, and will now mate and start other nests. Ants have limited flying ability during the mating process, Harold explains, but ants of that size would be able to travel a large distance. In top-secret conferences, the Medfords, Bob, Ben, Kibbee and O'Brien meet with Washington officials. After showing film footage demonstrating the strength, ferocity and mating habits of ants, Harold predicts that humans will be extinct within one year if the queens are not destroyed. Secrecy is maintained to avoid worldwide panic, but news is monitored for unusual sightings and mysterious disappearances or deaths. When ant-shaped flying saucers are reported by Texas ranch foreman Alan Crotty, who is then institutionalized, Bob knows that the man is not insane, but to keep the story from spreading, tells his psychiatrist that the FBI will let him know when his patient is well. Having assumed that, so far, only the American continents are in jeopardy, the Medfords and their colleagues are disturbed by reports that a ship on its way from Mexico to Singapore became infested with giant ants that killed all hands. Shortly after the ship is sunk to kill the queen and her offspring, forty tons of sugar is ripped out of a railroad car in Los Angeles. Thinking that the second queen is the culprit, Harold and his colleagues go there to investigate and learn that a man, who was last seen flying model airplanes with his two sons, died mysteriously and his children are missing. From a hospital room overlooking the Los Angeles River, Jenson, a half-coherent drunk, reports that he saw the family and the giant ants near an opening that leads to 700 miles of tunnels under the metropolis. Martial law is instated and the Army is called in. However, because they believe the children are in the tunnels with the ants, they cannot gas or burn out the creatures. Instead, armed with bazookas and flamethrowers, Ben, Bob and Kibbee ride jeeps into the tunnels with the soldiers. After finding the boys alive in a storm drain, Ben gets them to safety, then is killed by an ant. Later, Bob radios to the waiting Pat and Harold that new queens have not hatched in the egg chamber. He orders the chamber burned and the crisis is over. However, Bob later wonders if more mutations from later tests will be discovered. Harold responds that when man entered the atomic age, he opened a door to a new world and what will eventually be found in that new world no one can predict.