Despite speculations that recent events in outer space would cause earthquakes or other catastrophes on Earth, nothing of the sort occurred. However, Ernest Hubbs, a biologist, has detected a marked change in a community of ants located in upland Arizona. Ernest writes a memorandum to Al Flanders Smith of the National Science Foundation Committee on Biological Controls to announce his findings: traditional antagonisms are no longer taking place in the ant community he has been observing, causing the population to increase. In addition, certain predators, like praying mantises and spiders, have disappeared. Ernest predicts that the ant population will grow uncontrollably in these current conditions and proposes that he set up an experiment station in Arizona to address the problem, with the help of a young scientist named James Lesko. Soon after, in Paradise City, Arizona, Ernest and James explore a house that has collapsed, possibly due to ants. After the scientists examine a set of six tall dirt columns in the desert that may have been built by the ants, Ernest gives a local resident, Mr. Eldridge, an evacuation notice. The Eldridges must leave the area while Ernest and James conduct their experiment. The scientists establish the headquarters where they will work and live in a remote geodesic dome powered by a generator. As they wait for ants to appear, the National Science Foundation keeps in touch via radio to pressure the men to work faster. One day, Ernest shoots the six dirt columns, causing them to collapse, while James detects ant noises on audio monitors inside the dome. At night, Eldridge wakes at the sounds of his panicked horse and discovers that ants have overtaken his farm. Eldridge shoots the crazed horse and flees his home with his wife, Mrs. Eldridge, his granddaughter Kendra, and Clete, a farmhand. As they drive away from town, Mrs. Eldridge becomes hysterical when she notices that the car is covered in ants. Eldridge stops the car and they run toward the scientists’ dome. When the ants destroy the generator outside the dome, a backup system allows machines inside to keep operating. James deduces that the ants are communicating, and that a central mass of ants is acting upon a command coming from one source. Meanwhile, Ernest activates a yellow spray that kills the ants surrounding the dome. The next day, Ernest and James don protective suits and explore the damage outside. They find Eldridge dead, covered in the yellow ant-killer that has now turned to powder. Although Ernest reacts indifferently, James is upset. Declaring that they will be safe for the next three or four days, Ernest unclenches Eldridge’s dead hand and ants crawl out of three holes in the man's palm. Eldridge’s granddaughter, Kendra, emerges from an underground bunker nearby and faints at the sight of her dead grandfather. Back inside the dome, Kendra, James, and Ernest shower off before re-entering the main area. Ernest begins experimenting with some ants inside a closed laboratory, subjecting the insects to cold, heat, starvation, and predator threats in the form of praying mantises. Upset and confused, Kendra enters the laboratory and smashes the glass tubes that contain the ants, allowing them to escape. Ernest, whose hand was bitten by one of the ants, closes off the laboratory room and sprays the yellow poison inside. However, some ants survive, eating the yellow ant-killer, and, later, laying yellow-colored eggs. One day, outside the dome, several dirt structures appear, reflecting sunlight onto the dome so that it heats up. James worries that he, Ernest, and Kendra will fry inside, but Ernest seems unconcerned, remarking that the ants have adapted beautifully to the threat he and James have posed. Ernest shows James some yellow ants on a video monitor, explaining that they resulted from the ants who ate the yellow poison. James wants to call for rescue, but Ernest argues that they must stay and combat the ants. When James tries to radio the National Science Foundation, he realizes that the ants have cut off their radio signal. After noticing that the ant bite on Ernest’s hand has swollen into a large mound, James broadcasts a loud, high-pitched signal to deter the ants. Ernest tells James he is not feeling well as the dome machinery overheats and malfunctions. The temperature inside the dome nears 120 degrees Fahrenheit, and James wonders how the ants know how to attack their most important machinery, but Ernest seems unsurprised. At night, the equipment functions again temporarily, and James sends a signal to the ants, a sound that translates into a simple square. James tells Ernest that math is the universal language of intelligent creatures, and if there is intelligence amongst the ants, he wants them to know that he and Ernest are intelligent as well. As James and Ernest lie awake one night, James wonders why the ants don’t kill them, and Ernest says their only hope is to kill the queen ant. On the video monitor, Kendra sees a mass of ants attack a small rodent at lightning speed. James interprets a message he receives from the ants, deducing that the ants want to talk to someone who is inside the dome. In turn, Kendra ventures outside, sacrificing herself. The next day, James finds a note left behind by Kendra that reads, "You’re free now." Ernest walks outside and James follows him. As Ernest heads toward the area where he believes the queen ant is stationed, he falls into a hole and a swarm of ants devours him. Sometime later, James puts on his protective suit and walks through a field, spraying a new, bluish substance to ward off the ants. Believing that the ants will overtake the desert and, later, cities, James goes in search of the queen ant, hoping to kill her himself. He slides down a massive hole in the ground and finds Kendra. Noticing a change in Kendra, James realizes the ants have converted her to their side. James believes that he and Kendra are being primed to become part of the ant world, and although they are unsure for what purpose, he is certain that they will be told.