After a spectacular and mysterious cosmic event, ants of different species undergo rapid evolution, develop a cross-species hive mind and build seven strange towers with geometrically perfect designs in the Arizona desert. Except for one family, the local human population flees the strangely acting ants. Scientists James R. Lesko and Ernest D. Hubbs set up a computerized lab in a sealed dome located in an area of significant ant activity in Arizona. The ant colony and the scientific team fight each other, though the ants are the more effective aggressors.
The narrative uses the scientific team as the main protagonists, but there are also ant protagonists going about their duties in the colony. The ants immunize themselves to the humans' chemical weapons and soon infiltrate their lab. Teams of ants penetrate the computers of the lab and short them out. After Lesko decodes an ant message, Kendra Eldridge (a young woman who has taken refuge with the scientists), becomes convinced that her actions have enraged the ants. Seeking to save the two scientists, she abandons the lab and apparently sacrifices herself.
Hubbs and Lesko begin to have different plans for dealing with the ants. While Lesko thinks he can communicate with the ants by means of messages written in mathematics, Hubbs plans to wipe out a hill he believes to be the ants' central hive. Delirious from a venomous ant sting, Hubbs can barely get his boots on, but is determined to attack the hive and kill the ant queen. Instead, Hubbs literally falls into a trap – a deep pit that the ants fill with earth. Helpless to save Hubbs and convinced that the ants will soon move into desert areas where their growth will exceed man's ability to control them, Lesko chooses to follow Hubbs's plan. He sets out to the hive with a canister of insecticide. Descending into the hive, Lesko hunts for the queen, but instead finds Kendra reaching out from under the sand. The two embrace and Lesko realizes that, far from destroying the human race, the ants' plan is to adapt the human race and make them a part of the ants' world. In a voice-over, Lesko states that he and Kendra do not know what plans the ants have, but they are awaiting instructions.
