In 1967, a squad of military investigators in full NBC suits examine an African village where many are dead or dying. They depart in a helicopter and shortly after a plane flies toward the village and drops a fuel air bomb and immolates the entire area. White faced monkeys scurry off.
Inside a high security lab people work in a variety of containment zones.
Colonel Dr. Sam Daniels (Dustin Hoffman) is washing his dogs and gets a call from General Billy Ford (Morgan Freeman), a class 4 illness has been found in Africa, they want to get there before the WHO. Sam drops his dogs off at his estranged wife's house, she, Dr. Robby Keough, (Rene Russo) is moving to Atlanta for a job with the CDC.
Loading up a Herc, Daniels is surprised one of his team is not there. Gen. Ford is there and gives Sam a file on his new man, Major Salt (Cuba Gooding).
On the flight Daniels and Casey Schuler, (Kevin Spacey) quiz Salt, he has never seen a haemorragic fever up close. At a village, the team gets off helicopters, in full suits, to walk through a village. They enter a tent with many dead bodies. Salt sees a child with two dead parents and panics, tears off his helmet, a man arrives and says it is OK, it is not airborne. Daniels and the man discuss the illness, patient zero was a worker who went to work with the white man logging the Forest. The local juju man thinks this released an evil. The helos fly off as the village is torched.
On the return flight, Daniels calms down a shaky Salt.
Back home, Robby is upset she had to look after the dogs longer than planned. Sam agrees to give her both dogs as she moves to Atlanta.
A ship sails across an ocean.
Casey and Sam discuss Robby and prepare to enter the level 3 lab, Sam has not noticed a small tear on his suit. Casey chides him and makes a repair with duct tape. In the lab, Salt has isolated the Motaba virus and shows projections of how fast and deadly it is. The men are in awe.
Ford goes to a class 3 lab and recovers samples from deep freeze..
General Donald McClintock (Donald Sutherland) and Ford see the results of the analysis, it is the same virus as 1967. McClintock wants it covered up and Daniels taken off the case. The next day Ford tells Daniels he is needed in New Mexico. DAniels argues they have already started gene mapping it.
A young man, Jimbo Scott (Patrick Dempsey) takes a monkey from customs quarantine in San Francisco.
Daniels calls Robby to issue an alert as all the test animals are dead, she refuses as he only has a hunch at this point.
A man Rudy Alvarez works at a pet store and receives the caged white faced monkey, but refuses to buy it as he wanted a male, it scratches him and contacts another monkey.
Robby discusses the alert with her boss, he dismisses it.
Jimbo frees the monkey in the redwood forest.
Jimbo is feeling sick on a plane, he gives a kid a leftover cookie, but his mother stops the kid from touching it. In Boston he greets and kisses his girlfriend, then faints. At the pet shop Rudy collapses and is taken to hospital, unresponsive.
In a lab a distracted tech breaks sample vials and blood splashes in his face.
After reading daily reports, Robby notices and decides to come to Boston. She tries to interview Jimbo but he dies. His girlfriend is also sick and soon dies. RR autopsies Jimbo and is shocked, she calls Sam to discuss. She knows Jimbo worked in a quarantine facility in San Jose.
At a movie theatre Henry the lab tech coughs, then goes into paroxysms in the lobby.
The monkey enjoys the wilderness and clear skies in California. Henry is in hospital but not quarantined. More sick people overwhelm the small hospital. Robby and her team cheer when the find out no one else on the plane has been sick, but then receive word of the California outbreak.
Ford and Daniels argue, Sam wants back on the case but is being assigned to New Mexico. At the airbase Sam convinces the air tech his orders are changed to California.
McClintock and Ford talk on the phone, McClintock urges they continue a conventional response and not reveal the 1967 info.
A large army force enters and quarantines a small town, Cedar Creek. Robby and her team arrive escorted by police. In full suits they enter the hospital, she meets Sam there, he has assumed local command. There are many sick, from the movie theatre. They also find a man with pustules who has been sick a week. Daniels now suspects it is airborne.
Gen. Ford meets an army Colonel Briggs (Dale Dye) who confirms they have a full cordon.
Maj Salt shows the new strain is changed slightly. They discuss with Robby and suspect a host animal with two strains of the virus. Alvarez and the pet store seem to be a key.
Daniels reports to Ford on the severity, 19 dead and hundreds sick, and is angry that Ford seems complacent. The media hovers and reports from the perimeter.
Robby and an assistant break into the pet store, find a sick monkey but Robby says it can't be the host. In town, some locals try to break out in pickups but are shot up by the army with extreme force.
Salt reports the monkey has the original strain. Sam says to keep testing and looking. The army starts a curfew and tightens control on the town.
In the hospital Sam finds Ford there and a new intravenous drip, E-1101 being used. Ford says it is an experimental drug, he is trying to help. DAniels brings a E-1101 bag to Salt and asks him to find out what it is.
A tearful woman leaves her house and is taken away in a Hummer. Sick people are being taken to a common site.
Schuler looks at blood samples, numbers in the 600s, and angrily says all are positive, the entire town is infected. A tent city is built on the town sports field.
Tensions rise as there is no record of any other monkeys or missing animals. In the portable Class 3 lab Schuler has a panic attack, he has cut his suit accidentally but doesn't tell Robby.
At the Pentagon, Gen. McClintock describes a worst case spread of the infection. The men at the table discuss Operation Clean Sweep, firebombing the 2600 residents of the town. The Chief of Staff (JT Walsh) is angry and demands everyone agree unanimously for such drastic action.
A barn is torched. The monkey arrives at the window of a sleeping girl.
Ford and McClintock discuss the 1918 pandemic and other wartime bombings. McClintock has approval for Clean Sweep and says the town folk are casualties in a war.
Robby and Sam are frustrated in how Jimbo got sick. Suddenly they notice the pet store monkey is alive and well. DAniels realizes E-1101 is a cure for the original strain, the army had it all along. Casey then goes into paroxsyms and is rushed to the hospital. Robby punctures her glove trying to give Schuler an injection and rushes to try and wash off.
Daniel rushes to confront Ford, saying he could have stopped it earlier, they were trying to protect a perfect biological weapon. Ford tells Daniels they have to do their jobs, Sam realizes they will wipe out the town. Ford admits the President has given the order for later that day.
Salt now calls Daniels to report Jimbo smuggled an animal from Customs.
Gen. McClintock demands Daniels be arrested.
Daniels warns Robby to leave town by 1800 hrs if no symptoms have shown. He reminds her all the troops are leaving.
Daniels and Salt change into regular uniform and escape in a scout helicopter. McClintock says to shoot it down.
Daniels and Salt arrive in San Francisco and demand customs records for every ship. They figure out the ship they want has just left harbour, they fly off in pursuit.
At a house a mom asks her young daughter where the monkey came from in a crayon drawing she made.
A nervous Robby checks herself for signs of illness.
Salt finds the ship in heavy fog, he can't land but gets close for Sam to jump. He makes it. The crew are all Korean but understand he is a doctor, they show him a dead man in the freezer. Sam inspects the man's bunk and finds photos of him and a monkey.
Casey is near death, Robby is looking flushed and holds his hand.
Salt and Daniels arrive at a TV studio and barge onto the news set. They want help in finding the monkey and show photos. The mother realizes her daughter has seen the monkey.
Salt and DAniels now fly to the house in Palisades. McClintock reams out Colonel Briggs and also flies out in a pair of gunship helicopters.
Sam tries to convince the young girl to help them catch the monkey.
Gen. Ford puts out a verbal message to all troops to do their duty, etc. The bomber plane begins to taxi.
The girl calls for the monkey as the adults stay in the house. Daniels checks his watch. Salt has a tranquilizer pistol ready. He stumbles but takes his shot and gets the monkey with the dart. Daniels reports to Ford he has the host and to stop the bombing, Ford agrees to buy some time but to expect some resistance.
Now McClintock in his helo lines up and threatens to shoot down the scout helo. The three helos have a low level chase in a river bed. Maj Salt, an expert pilot, escapes.
They land in the deserted town Cedar Creek, Salt is to start making an antivirus in the portable lab. Sam suits up and goes to the hospital, Robby is now near death. Sam removes his hood and let's her touch his cheeks. Salt arrives with an IV bag, Sam hooks it up to Robby and tells Salt to make more.
McClintock returns to the Command Post and re-issues the order to bomb the town. In the hospital Robby's vitals are coming back to normal. Salt says it is too late, the bomber is coming. They fly off in their scout helo to convince the bomber pilots. Daniels radios the bomber and tries to explain he has an anti serum, to abort the mission. Ford radios a clue in to fly into the path of the bomber. The helo hovers in the flight line and at the last second the plane veers and drops the bomb in the nearby ocean.
Ford takes over from a hysterical McClintock and relieves him of command. Col Briggs arrests the General at gunpoint.
In town, people are walking about. Robby wakes, Sam has had his dose of antiserum. The two reconnect.