Ray is residing at a "friend's" house and preparing breakfast for himself while listening to classical music. Meanwhile, a pale sweating man is driving a truck toward the house and weaving all over the road. The man staggers to the door and hits the buzzer, and collapses into Ray's arms. He says for Ray not to touch him and mutters "mutated smallpox," then dies. Ray quickly reads up on how to deal with smallpox: clean thoroughly, burn all clothing, improvise a mask. He checks the man's ID and determines he's Louis Kelter with the World Health Organization (WHO). He then puts Kelter's corpse in a freezer, takes blood samples, then seals it with duct tape. Ray then douses man's car with gasoline and sets it on fire.
Ray then calls another "friend," Dr. Vance, and calls in a favor. He goes to a sound studio and seals himself in with duct tape, then turns down the temperature as Dr. Vance arrives and reveals there is no vaccine for smallpox because there is no longer any smallpox. Ray explains what happens and tells Vance to check out the blood sample. Vance has checked and there's been no reported case of smallpox in fifteen years. The WHO keeps a small sample of smallpox just in case but Ray asks him to check as much as he can. Ray refuses to go to the hospital for fear of spreading it and waits while Vance checks the sample. He then calls David Warren, another doctor with the WHO and special assistant to the President, and calls in a favor to find out about the WHO. When Ray threatens to go to the press, Warren admits that six cultures went missing and it's been hushed up by the government under Congressman Hartzler's subcommittee. Warren promises to check it out and Ray waits for Vance to finish with the samples.
Several hours later, Vance reports that Ray's okay. The smallpox can gestate and die within four hours, and the process is accelerating. Vance figures that Ray is out of the woods but says he's had no luck getting the vaccine. Ray again refuses to go the hospital and instead goes to the Federal Building and attaches a remote device to the automated gate. He then sabotages the staff cars and goes in to confront Hartzler, claiming to be a reporter. Ray grills him about smallpox virus and gives the location of Kelter's body, but Hartzler denies knowing anything. Ray seems convinced... but then rips off Hartzler's sleeve to reveal he's had a recent smallpox vaccination. Hartzler calls security to take Ray away then calls in a team to recover Kelter's body. Ray knocks out the guards and runs outside to his car. The guards try to pursue in the sabotaged cars without success. They try to pursue on foot but Ray opens the gate by remote then closes it and makes his escape.
Hartzler's team arrives at the house in protective gear and recovers Kelter's body, then leave. Ray follows them in and slips in to the autopsy wearing a protective suit to conceal his identity. Dr. McGill is supervising the examination and sends Ray to get a blood workup, then meets with Hartzler. Ray slips into McGill's lab and finds several bottles of vaccine, and injects himself with a dose. McGill takes Hartzler to his office and Ray turns on the intercom and slips into the next room. As Ray listens in, McGill explains that Larry Thorson, another scientist on the project, panicked when Kelter traced the theft of the cultures to Hartzler's group who were conducting illegal biological warfare research. One vial was broken during the struggle and both of them left. The guilty Thorson took the remaining smallpox with him to bury and they don't know where he is. McGill warns that once the smallpox cultures hit the air, it could spread uncontrollably and kill millions. Hartzler insists on keeping the entire affair covered up. Meanwhile, Ray finds Thorson's checkbook and sees a payment made to a concrete company.
Ray drives to the Thorson's home address in Newcomb but finds the small town entirely decimated by smallpox. McGill's team flies in and Ray quickly hides, as Hartzler and McGill check out the town, and determine the virus has accelerated and is now harmless. Ray knocks out several men then holds Hartzler at gunpoint. Another man holds a gun to Ray but Hartzler tells his people to back down and Warren arrives to take control of the situation on behalf of the President. He arrests Hartzler and places the town under martial law, and McGill warns that they've seen only the least of the potential fatalities if Thorson accidentally shatters another vial.
Ray and Warren go to Thorson's house and they find a broken vial that Thorson dropped. Ray is starting to weaken and Warren suggests he get into a hospital. It turns out Ray was undercover in the WHO for six months and then disappeared on Warren. Ray finds a book on nuclear fusion and concludes that Thorson is going to bury the vials at a local power plant. They take a helicopter toward the plant near the local reservoir and spot Thorson, who plans to bury the remaining vials in the center of the reservoir. He tries to warn them off and panics as they approach. Ray has Warren take the controls and jumps to the reservoir, then tries to convince Thorson to stop. The delirious Thorson thinks that Ray is one of "them." Running away, he trips and spills the vials, and Ray manages to catch one just before it falls into the water below.
Later at the hospital, the doctor reveals that Thorson should recover because of all the vaccine he took. Ray is in poor condition and Warren asks to see him. However, when they go in they find that Ray has left, leaving only a note for Warren saying he owes him one.