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After a space satellite launched by the United States as part of a top-secret biological research project code-named SCOOP crashes near the small town of Piedmont, New Mexico, two military recovery technicians arrive. When the men report their discovery of two dead bodies to Vandenburg Air Force Base mission control, they are ordered to return immediately, but the controllers then lose contact with the men. A reconnaissance photography flight over Piedmont reveals dead bodies scattered throughout the small town, prompting duty officer Maj. Arthur Manchek to declare a state of emergency and summon a special scientific investigative team that includes pathologist Dr. Charles Dutton, microbiologist Dr. Ruth Leavitt and surgeon and blood chemistry expert Dr. Mark Hall, led by Nobel Prize-winning biologist Dr. Jeremy Stone. Stone is privately briefed on SCOOP, created by the army's Biological Research Division to collect organisms existing in outer space that could be used as potential biological weapons. The morning after the satellite crash, Stone and Hall, wearing protective gear, are flown by helicopter to Piedmont. Examining several bodies, they conclude that some victims died quickly while others appeared to have had mental breakdowns before dying. As the pair proceeds through the town, Hall notices a car accident victim whose injuries did not bleed. The men track the satellite to the town doctor's office, where Stone is indignant to find the capsule has been opened. Hall then inspects the dead physician and when he cuts the man's arm, powdered blood pours out, revealing clotting throughout the entire system. Recognizing that whatever infected the citizens of Piedmont is not from Earth, the men prepare to depart with the satellite when they are startled by a sound. At a nearby house they find a live baby crying lustily. Urged on by their protective suits' dwindling oxygen supply, Stone summons the helicopter, which air-lifts the baby aboard. Hall is then nearly attacked by an old man brandishing a cleaver but when the man collapses on the ground writhing in pain, he is also taken aboard the helicopter. Stone contacts Manchek to request that Piedmont be "neutralized" by a thermonuclear blast to prevent the spread of the mysterious infection. While Stone, Hall and, separately, the baby, old man and satellite are transferred to a secret location, Manchek requests authorization to destroy Piedmont. Science advisor Dr. Robertson immediately agrees, but political advisor Grimes insists on a more cautious approach. A little later, Manchek receives a call from the President telling him to delay the destruction of Piedmont for twenty-four to forty-eight hours. Stone and Hall then meet Dutton and Leavitt in a remote desert area near Flatrock, Nevada where a nondescript government agricultural station masks the entrance to Wildfire, a five-level, underground biological crisis laboratory designed in part by Stone two years earlier. Stone is puzzled to learn from the communications center that there has been no message from the White House regarding Piedmont, but with the others, begins a sixteen-hour decontamination procedure that takes them through each level of Wildfire until they meet on the lowest, safest level to study the two survivors and the satellite. Using a special key, Stone arms the laboratory's nuclear device, which would destroy the facility should contamination threaten to break out of Wildfire. Stone then presents Hall with a similar key, explaining that as a single male, Hall is the "odd man" selected to carry the only key that can stop the nuclear detonation, which is on a five-minute delay after being triggered. After the long decontamination procedure is completed, Stone and the team go over their objective: to confirm there is an entity, uncover its structure, then contain and control it. While Hall visits the two survivors, Stone and Dutton examine the satellite using robotic hands, which allows them to work from the safe confines of their sealed lab. When live test rats and a monkey exposed to the satellite die shortly thereafter, Stone and Dutton conclude that the organism is transmitted by air. Joined by medical technician Karen Anson, Hall uses a protective body sleeve that shields him from direct contact with his patients and examines the baby and old man. Meanwhile, Leavitt joins Stone to conduct high-magnification scans on the outside and inside of the capsule. Blood tests from the old man, who has revived momentarily to identify himself as Jackson, indicate that he is anemic and has a high level of acidosis. Jackson admits he drinks the alcoholic fuel sterno to quell the pain from a bleeding ulcer, which further confounds Hall. Dutton's autopsy and test results on the lab animals demonstrate that the organism is inhaled, clotting blood in the lungs before spreading outward into the rest of the body. Later, Stone and Leavitt's scans reveal a tiny indention made by a grain of sand that is covered with green patches. Under high magnification, Stone and Leavitt are startled to see the green patches move and grow. Back at Vandenburg mission control, Manchek learns that an Air Force training mission jet crashed near the Utah and New Mexico state lines and the pilot's last frantic transmission declared that all the rubber in the craft was dissolving. Frustrated at not having heard from Stone about the delay to destroy Piedmont, Manchek and several experts visit the crash site and conclude that an organism that consumes synthetic rubber destroyed several parts of the plane. Back at Wildfire, after running more tests, Stone, Dutton and Leavitt are astonished to find that the green substance resembles plastic, and although it contains no amino acids, proteins or enzymes, it still grows. Working well into the third day, Leavitt begins monitoring cultures of the organism to search for growth patterns. Unknown to the others, Leavitt suffers from epilepsy, and when a computer message flashes in red indicating growth, the blinking sends the scientist into an epileptic trance. When Leavitt revives nearly half an hour later, the testing cycle has ended and she realizes that she has missed several results. Meeting at the start of the fourth day, Hall reveals Jackson has identified the baby as Manuel Rios and said the infant cried continually. Stone then messages central control to inform them an organism has been isolated and an automatic response sends back the assigned name for the life form as "Andromeda Strain." Standing by the teletype machine, Hall glances at older messages and excitedly shows Stone the original message from Manchek regarding the postponement of the destruction directive. Unaware that a sliver of paper had prevented the message alarm bell from ringing for Manchek's priority messages, Stone angrily contacts the White House to demand action be taken at Piedmont. Grimes defends the President's caution and Robertson asks what the team thinks of the jet crash. Energized by the information from the crash, Stone sends the others back to work and within hours they determine that the organism's structure is crystalline. Leavitt reports that Andromeda grows well in oxygen, but grows best in pure carbon dioxide and hydrogen. With a shock, the scientists suddenly realize that these results mean that a thermonuclear explosion would allow Andromeda to multiply at a fantastic rate, destroying the entire planet. Stone frantically contacts the White House to insist the destruction of Piedmont be called off. Relieved, the scientists return to their study and are mystified when Andromeda's dividing and mutations continue to occur, overloading the computer. As Hall and Karen continue to wonder what protected Manuel and Jackson against Andromeda, a yellow alert sounds, indicating that contamination has broken out in a localized area. Hall meets Leavitt in the hallway and as they rush to the main lab, the flashing lights set off a major epileptic seizure in Leavitt. Hall immediately recognizes the symptoms, but technicians and nurses, fearful that Leavitt has been infected by Andromeda, flee in fright. Eventually, Karen provides Hall with an injection for Leavitt. Hall then meets Stone in the main lab to discover that Dutton's pathology lab is contaminated. Terrified, Dutton sits panting heavily, monitored by Stone and Hall. Hall recognizes abruptly that labored breathing changes blood chemistry, which would occur in a crying baby and the agitated, drug-addled Jackson. Baffled when Jackson and Manuel's blood tests do not show exact opposite readings as they should, Hall orders Stone to cut the oxygen to Dutton's lab and tells the pathologist to keep breathing hard. Certain that Andromeda must experience a period of no growth, Hall begins running the growth results, reminding Stone that Leavitt may have had an epileptic blackout while monitoring the readings. The scientists then notice a test rat in Dutton's lab has gotten loose but shows no effect of Andromeda and conclude that the organism has mutated to a non-lethal form. At that moment, alarms sound and the computer warns that Andromeda has infected the ventilator shaft, where it is destroying the plastic. Moments later, Wildfire's protective nuclear device is triggered. Horrified, Stone and Hall race to the hallway, but automatic emergency procedures seal access to the safety station and the elevator to the next level. Stone urges Hall to take the ladder in the central core up to the next level before it is contaminated. Knowing that gas and lasers protect the core, Stone rushes to the computer room monitor to help guide Hall up the ladder. In the core, Hall evades several laser shots but is stunned by a grazing shot to his cheek and hand. Dulled by the pain, Hall reaches level four too late, as it has already been contaminated and its safety station sealed. With Stone's encouragement, Hall finally reaches the safety station on level three with nine seconds before detonation. Hall revives the following day and Stone, Dutton and the recovered Leavitt explain that the now-benign Andromeda has continued to grow into a super colony, but is being infused with silver iodine which will force it into the ocean where the heavy alkaline will destroy it. Two months later in Washington, D.C. at a closed hearing of the Senate Committee on Space Sciences, Stone details the events surrounding the discovery of the Andromeda Strain but asks what will happen when the next biological crisis occurs.