A man in army fatigues is driving a truck near Faultline, California. He becomes extremely ill, and this causes him to veer off the road and black out.
At FBI HQ, Bill listens to Carlisle's briefing on the man. He is Harvey Locke, a security guard with several arrests, dishonorable discharge, and a pro-war agitator. Locke is now in a stable condition in hospital. His illness has not been diagnosed, but it is believed to be contagious and he is in quarantine. His truck contained a machine gun, the same type that was recently stolen from a federal armory. The FBI suspects Locke is connected to a right-wing mercenary gun-running terrorist organization, and they want the rest of the guns and the people responsible rounded up. So Carlisle wants a volunteer to infiltrate the organization. The trouble is, the volunteer will risk contracting the same disease as Locke by coming into contact with his associates, and will therefore need inoculations. Bill volunteers for the job and is given blanket inoculations (plague, dengue fever, etc) as they do not not yet know exactly what they have to inoculate against. Afterwards, Bill's colleagues come into his office and give final farewells to him which give the impression they are not optimistic about his return.
At school, Ralph is helping with basketball practice, but the students start arguing and it comes to blows. Things go too far when Ralph takes a punch. Bill comes in and tells Ralph about his gun-runnning case. Ralph hopes this will not interfere too much with his upcoming weekend plans with Pamela. Bill wants to wrap it up before then as he is worried that whatever Locke has will reach epidemic proportions, and Bill has the impression that it may be the plague. Ralph is worried that he may get the plague from this case. Bill assures him that the suit will protect him as the aliens must have thought of including an immune system in the suit, and he himself has had inoculations. They head out to the nearest gun club, figuring it will be a good place to start looking for the paramilitary types they are looking for.
At the gun club, Bill enquires about Harvey Locke. The attendant has never heard of Locke. But Bill and Ralph immediately draw the attention of some of the men, who find out from the attendant that they are looking for Locke. The men immediately alert someone over the radio that someone has just tapped into their line. When Bill and Ralph leave the gun club, they are followed.
Bill and Ralph arrive at their motel, where Ralph spots Pamela's car. Bill is annoyed with the possible breach of security. Ralph tries to talk to Pamela alone and warn her about the possible plague threat. Meanwhile, the men from the club arrive, break into Bill's unit, knock him out and abduct him. Ralph spots them and changes into his suit to follow them, but he loses them.
Meanwhile, the men bring Bill to their base. It is a military-based cult. The leader is referred to as Bunker (but this may be a nickname as the actor is not credited as Bunker). Bunker finds Bill's FBI identification, but Bill manages to keep his cool and bluff Bunker about backup which he claims are now surrounding the area. Bill also manages to turn on his radio transmitter, so Ralph can overhear what is going on and home in. Bunker decides to test Bill's backup claims with the radar, which turns up nothing. Bunker spots Bill's inoculation marks and mistakenly assumes the FBI knows about the smallpox; so the disease is smallpox, not plague. Bill sees inoculation marks on the arms of the men.
Then a blip appears on the radar, the smallest blip the operator has ever seen. It is, of course, Ralph. The blip disappears, but because Ralph hit the fence and set off an alarm. Ralph jumps over the fence, setting off land mines and more alerts as he goes, and scaring Bunker enough into evacuating the base. Bill is heaved into Bunker's helicopter, and when he refuses to talk, Bunker hangs him out of the door of the helicopter to scare him into cooperation. Bill still refuses to talk, so Bunker orders his men to let him fall to his death. Ralph saves Bill, but they lose Bunker.
The FBI has put Bill on communications silence, so they cannot alert Carlisle except in person. Ralph also thinks he is starting to exhibit smallpox symptoms, but Bill thinks hypochondria is more likely. Ralph's hypochondria gets worse when Pamela starts reading out the symptoms of smallpox. Pamela also reads that smallpox is considered extinct, which raises questions as to why Bunker is giving his men inoculations against an extinct disease.
Back at the FBI, Carlisle tells Bill that Locke has died, and was diagnosed with smallpox. The United Health Organization (WHO) is on top of the case, but it is top secret as there is insufficient vaccine against a disease considered extinct. Bill also learns that his inoculations did not include smallpox as the disease is considered extinct. Upon hearing he was exposed to potential smallpox without protection, Bill gets worried that he will get smallpox and starts imagining symptoms as well. But he wants to stay on the case, so Carlisle sends him to Dr. Kelly of WHO, as Kelly is the best man to evaluate the information they have.
Meanwhile, Bunker is giving battlefield speeches to his soldiers about how their enemies, including those who are ruining the country, will suffer from the smallpox. It is revealed that revenge is part of the agenda as Bunker lost his comrades to Japanese soldiers. He leads them off into "deadly battle."
At WHO headquarters, Kelly advises Ralph and Co that Locke must have developed full-blown smallpox because the inoculation he received was injected improperly. Kelly then informs them that there are three laboratories in the world that hold the smallpox virus in quarantine for research purposes, and one of them is in Needles, California. They realize that Bunker intends to steal the virus and use it as a biological weapon. Pamela also tells Kelly about Ralph and Bill's concerns that they have smallpox. Kelly informs them that smallpox takes at least two weeks to show. All of a sudden, Bill and Ralph are feeling better. WHO then gives them smallpox inoculations.
Kelly tries phoning the laboratory to warn them, but Bunker's men have blown up the telephone poles. They are soon sending their helicopters in and cutting through the fences. Ralph slips away to change into his suit and fly over to the laboratory while Bill gives instructions for alerting Carlisle about the paramilitary attack on the laboratory. Kelly and Bill head out to the laboratory in the WHO helicopter. They arrive ahead, but Bill has a bad feeling because it is too quiet. Sure enough, Bunker and his men have captured the laboratory and now capture Bill and Kelly as well. They are brought to the laboratory, where Bunker now has the smallpox vial. Bill gloats to Bunker over the surprise that he survived Bunker's previous attempt on his life. Bill then asks Kelly what happens if the vial breaks. Kelly replies the virus will be contained if the laboratory is airtight.
Ralph arrives and takes down the guards outside. In the laboratory, Bill then starts urging Bunker to surrender, claiming that the area is surrounded. Bunker is not impressed as Bill tried something similar before. A scuffle ensues, which sends the vial flying through the air, and it will smash if it hits the floor. Ralph holographs it, smashes his way through and grabs the vial in the nick of time. He and Bill then take out Bunker and his men. Bill marches them into the waiting arms of the authorities. Bill lets Carlisle go on wondering how he captured the men single-handed (Ralph had slipped away before the authorities arrived) and wangles two weeks' vacation.
However, Bill's two weeks' vacation is spent in quarantine with Carlisle, and with Pamela and Ralph, who are making the most of it with lovemaking and no school stresses for Ralph. They are then told they will released from quarantine as long as they do not have any symptoms. But they must report to the authorities if they show any, for it can start with a sneeze. Then Bill sneezes. He says it is just a head cold, but everyone starts backing away from him.