Dr. Sheila Casper is summoned to the sleepy desert town of Gallup, Texas, where unexplained bat attacks have caused several grisly deaths. When night creeps in, swarming hordes of bats fill the darkening sky and invade the town. The bats swoop down and attack every living thing in their path, turning the town into living nightmare where everyone is a target and there is nowhere to hide.
Sheila and her assistant, Jimmy (Leon), team up with the local sheriff Emmett Kimsey (Lou Diamond Phillips) to try to find a way to stop the bats. They discover that a scientist (Bob Gunton) has tampered with nature and infected the bats with a genetic virus, causing the usually harmless mammals to become vicious killers. They catch and tag one of the bats, hoping it will lead them to their lair. However, these bats are too cunning. Seeking shelter from the dark, the team holes up in an abandoned high school when the bats unleash an unrelenting and vicious assault, seemingly in a coordinated attack.
When the sun gives them safety, Sheila and Kimsey locate the bats' roost inside an abandoned mine. With no way to defeat the bats' sheer numbers and power of flight, Sheila and Kimsey must bravely descend into the mine, where the bats hang from the mine ceiling asleep. If they can't stop the bats, night will fall, the bat colony will grow, the virus will spread, and the bats will take flight in search of more and more prey.