A group of soldiers led by Major Baker is ordered to investigate a basement level station which they believed was attacked. After Baker contacts his commander, General Slater, they begin to investigate who drove a civilian van into the base. It is revealed to be owned by a scientist named Dr. Bradford Crane, the only survivor of the attack. Slater orders two helicopters to check for a black mass (revealed as bees), but the two helicopters are swarmed by the bees and crash, killing the pilots inside. Crane insists to Slater that the base was attacked by the same African killer bees and destroyed the helicopters. Helena Anderson, one of the base's doctors, supports Crane's story.
Meanwhile, in the countryside, the Durant family is attacked by a swarm of the bees. The mother and father die from the bee stings, but Paul, their teenaged son, escapes in a Mustang. Although he is also stung, Paul manages to make it into town and crashes into the Marysville town square, where the citizens are preparing for the annual flower festival. The boy is brought into the hands of military personnel, where he hallucinates a vision of giant bees attacking him, due to the aftereffects of the bee sting. Wheelchair bound Dr. Walter Krim confirms to Crane that the very war they have feared for a long time has started against the bees. At the gates of the base, Slater confronts angry county engineer Jed Hawkins, who demands to see the dead body of his son, who was killed by the bees. Hawkins takes the body bag and departs, leaving the entire watching crowd silent over the loss. Slater suggests airdropping poison on the swarm, but Crane considers the ecological possibilities of the situation.
Recovering from his earlier bee attack, Paul and some friends go in search of the hive to firebomb it in revenge for his family's deaths, which results only in angering the bees, who make their way to Marysville and kill hundreds, including some children at the local school. Crane and Helena take shelter at the local diner, with pregnant café waitress Rita. Reporter Anne McGregor watches from the safety of her news van, hoping to get some exciting footage about the siege. After this most recent attack, Slater suggests evacuating many of the townsfolk in a train. However, the bees manage to besiege the train as well, killing several evacuees, including a love triangle made up of schoolteacher Maureen Scheuster, retiree Felix Austin, and town mayor Clarence Tuttle, who also runs the drug store.
Rita tries to board the ill-fated train, but is saved at the last minute by going into labor and is confined to a hospital bed. She gives birth to her child while also falling in love with the doctor in the process; but Paul suffers a relapse from the effects of being stung earlier and later dies, devastating Helena and sending her into a rage about why the children have to die. The savage swarm heads for Houston, and Crane decides to drop eco-friendly poison pellets on them, hoping that the swarm senses will harm them and stay away from the city. Unfortunately, the plan fails. Dr. Krim self-injects an experimental bee venom antidote to keep track of the results, although the trial proves fatal, he dies. Meanwhile, nuclear power plant manager Dr. Andrews is convinced that his plant can withstand the attacks of the bees, ignoring the warnings of Dr. Hubbard. However, at that moment, the alarm sounds and the bees invade the plant, killing both Andrews and Hubbard, as well as completely destroying the plant and wiping out an entire town.
Meanwhile, in downtown Houston, Crane analyzes tapes from the original bee invasion and comes to the conclusion that their alarm system attracted the swarm into the base. The bees invade once more, resulting in the deaths of Major Baker and Dr. Newman, one of Crane's associates. Slater uses a flame-thrower on the bees for Crane and Helena to escape, sacrificing himself in the process. Sonically altered helicopters successfully manage to lure the bees out to sea, where they douse the water with oil and set the swarm ablaze. Helena wonders if their victory was just temporary. Crane responds that he does not know, but decides that "if we use our time wisely, the world just might survive."
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