The story is told in flashback by Dr. Jeremy Stone, who is testifying to a congressional committee. After a U.S. government satellite crashes near the small rural town of Piedmont, New Mexico, almost all of the town’s residents die. A military recovery team tries to recover the satellite, but is unsuccessful. Suspecting that the satellite has brought back an alien organism, the military activates an elite scientific team.
Wearing protective suits, Dr. Stone, the team leader, and Dr. Mark Hall, a surgeon, are dropped in Piedmont by helicopter. They find that the town’s doctor had opened the satellite in his office and that all of his blood has crystallized into a powder. They soon discover that almost all of the victims’ blood has crystallized, causing rapid death. Two other townspeople have committed suicide after going insane. Stone and Hall retrieve the satellite and find two survivors — a 69-year-old alcoholic man named Peter Jackson and a six-month-old infant.
In addition to Stone and Hall, the elite team also includes Dr. Charles Dutton and Dr. Ruth Leavitt, who are summoned to a top-secret underground facility with the code name Wildfire, located in Nevada. Upon arrival they undergo extreme decontamination procedures, descending through four disinfection levels to a fifth level, where laboratories are located. If the organism threatens to escape, the Wildfire facility includes an automatic nuclear self-destruct mechanism to incinerate all infectious agents. Under the “odd man hypothesis”, Dr. Hall is entrusted with the only key that can deactivate the device, the theory being that an unmarried male is the most dispassionate person within a group to make critical decisions in a crisis situation.
By examining the satellite with powerful cameras, the team discovers the microscopic alien organism responsible for the deaths in New Mexico. The greenish, throbbing life form is assigned the code name “Andromeda”. Andromeda kills animal life almost instantly and appears to be highly virulent. The team studies the organism using animal subjects, an electron microscope, and culturing in various growth media in an attempt to learn how it works. Hall tries to determine why the elderly man and the baby survived.
A military jet crashes near Piedmont after the pilot radios that his plastic oxygen mask is dissolving. Meanwhile, Dr. Stone, who created the Wildfire laboratory, is accused by Dutton and Leavitt of designing the lab for biological warfare research. Unknown to other team members, Leavitt’s research on the germ is impaired by her undisclosed epilepsy.
Hall realizes that the alcoholic Jackson survived because his blood was acidic from drinking Sterno, and that the baby lived due to his blood being too alkaline from constant crying, suggesting that the organism, Andromeda, can survive only within a narrow range of blood pH. Just as he has this insight, the organism mutates into a non-lethal form that degrades synthetic rubber and plastics. Andromeda escapes the containment room into the lab where Dutton is working. Once all the laboratory’s seals start decaying due to Andromeda’s escape, a five-minute countdown to nuclear destruction is initiated.
Hall rescues Leavitt from an epileptic seizure, triggered by the flashing red lights of Wildfire’s alarm system. Meanwhile, the team realizes that the alien microbe would thrive on the energy of a nuclear explosion and would consequently be transformed into a supercolony that could destroy all life on Earth. Hall races against the laboratory’s automated defenses to reach a station where he can disable the nuclear bomb with his key. He endures an attack by automated lasers as he climbs through the laboratory’s central core until he finds a working station, disables the bomb, and then collapses.
Hall awakens in a hospital bed. His colleagues reveal that clouds are being seeded over the Pacific Ocean, which will cause rain to sweep Andromeda from the atmosphere and into alkaline seawater, rendering it harmless. The movie ends with Stone testifying to a U.S. senator that, while they were able to defeat the alien pathogen, they may be unable to do so in the future. The film ends by showing Andromeda dissolving in seawater and then forming the number 601, the Wildfire computer signal for information coming in too fast for the computer to analyze.