In the Middle East, Barney and Willy break into Interoco, a chemical manufacturing plant, by posing as soldiers. To get to the computer that handles production and sabotage it, the two agents have to go through the wall of an adjoining vault containing canisters of Dehominant-A, a lethal nerve gas. As Willy moves the canisters aside to clear a spot, he inadvertently knocks one open. When Barney unwittingly steps into the leaking puddle, his leg is instantly paralyzed.
Dr. Vazan and Colonel Leo Orlov, head of security, meet with General Skoplin, the government representative. Vazan informs Skoplin that thanks to the advanced computer that the government has provided, they have been able to develop Dehominant-B, an advanced version which causes death in eight seconds. They activate the computer and begin the extended process of developing the nerve gas in quantity.
Willy half-carries/half-guides Barney to the exit, telling the security guard that his teammate sprained his ankle. However, a doctor notices them and recognizes Barney's symptoms, and the security guard sounds the alarm before Willy knocks him out. As Orlov organizes his men, Barney tells Willy to get out and warn the others. Willy has no choice but to slip out past the guards and make his escape. Orlov and his men capture Barney and the colonel demands to know what he was doing. When Barney refuses, Orlov promises him a slow painful death if he doesn't talk.
Willy arrives at the team's hotel room and tells Jim, Dana, Paris, and Doug what happened. Doug, a doctor, warns them that Barney only has three and a half hours. Jim checks in with Washington and is told to continue the mission, and rescue Barney afterward. However, no one else on the team has the expertise to reprogram the computer. Jim comes up with the name of a computer expert, Dr. Jerry Carlin, who is visiting the area. However, he's a hippie dropout and Jim figures that he won't work for them voluntarily. Paris questions whether they have the right to involve an innocent, but Jim reminds the team that the government will use Dehominant-B to kill thousands and then goes to work on a new plan.
Jerry and his girlfriend, Judy Moore, are at a café in town. A waiter informs Judy that she has a phone call. She steps away to take it and Jim, posing as a government official, keeps her occupied with questions about her passport. Dana comes over and introduces herself to Jerry, and shows him that she has a complete dossier on his background. As Paris secretly takes photos of Jerry, Dana tells Jerry that the government has taken over Interoco and is manufacturing nerve gas. Jerry figures that one more chemical weapon won't make a difference and refuses to help Dana sabotage the computer. She tries to offer him money but Jerry refuses and tells her to go away. Before she leaves, Dana gives him her card in case he changes his mind.
Vazan tells the weakened Barney that the Dehominant-A is causing his body to deteriorate and offers him the antidote in return for his confession. Barney insists that he and Willy were working alone but Orlov doesn't believe him and withholds the antidote.
At the hotel room, Jim goes over the blueprints for the plant and says that the autopsy room is the best place to conduct their operation and that they can get to it through the furnace room.
When Orlov suggests that they give Barney a truth drug, Vazan assures him that their intruder will crack from the pain. Skoplin is called back to his embassy but first tells Vazan and Orlov to make sure that the nerve gas manufacturing goes as planned. As Technician Tirkin informs Vazan that they are 40% into Phase 2 of manufacturing, Vazan receives a call from Jim. Jim passes himself off as a passing acquaintance and says that Vazan is being considered for a Nobel Prize for his work in pesticides. He asks for permission to send Dana over to collect his notes for the nomination, but Vazan is reluctant to take time away from his project at a critical moment. When Jim hints that there are rumors that Vazan is performing nerve gas experiments, the scientist is quick to let Dana in and get his version of the truth out.
Paris and Doug pose as local narcotic officers and bust into Jerry's hotel room. They plant drugs in Judy's purse and arrest her, and Doug takes her away. Paris holds Jerry prisoner at gunpoint long enough to explain that Judy is facing ten years in a local prison. Jerry realizes that the whole thing is a setup and Paris claims that he's a local intelligence officer. He knows about Dana's meeting with Jerry on behalf of American intelligence and demands to know what she told him. Jerry insists that he knows nothing but Paris tells him to accept Dana's offer and find out what she's up to. With little alternative, Jerry agrees and Paris tells him that he'll contact him when he needs a report.
Jerry meets with Dana, saying he changed his mind because he needs the money. Once she gives him a haircut and trim, Dana takes Jerry out to the desert where the others are opening an access hatch to the water pipes leading from the sea to the plant. Paris and Doug are wearing gas masks so that Jerry won't recognize them from earlier. They enter the pipes with Jerry while Dana seals the hatch behind them and heads for the plant.
Vazan gets a report that the tanks are overheating and orders Tirkin to pump in seawater to cool them down. Water floods the pipes and the IMF team is forced to run for it. Once the tanks have cooled down, Vazan orders Tirkin to cut off the water flow. The IMF team manages to get past the closing valve just in time. Vazan then goes to interrogate Barney again and warns that if he waits too long, the antidote won't save him. Barney still refuses to talk and Orlov recommends that they let him die.
Willy and Doug put on soldier uniforms while Jim, Paris, and Jerry dress as plant workers. Doug escorts Paris to a closet containing pneumatic message pipes and then stands watch outside while Paris burn through a pipe with thermite. Meanwhile, Willy goes to requisition a light van.
Jim takes Jerry to the autopsy room and Jerry is forced to face the reality of the nerve gas when he sees the dead experimental animals. However, he still insists that one more weapon won't make a difference. Jim can't disagree but figures that his job is to keep one more weapon from coming into the world. He refuses to argue the matter further with Jerry and gives him the computer schematics.
After removing the pneumatic pipe section, Paris put a fake message cylinder in and reattaches the segment. The file clerk receives the cylinder, which contains ID confirming Jim and Jerry as Interoco employees. His assignment complete, Paris leaves with Doug.
Jim tells Jerry that he has to destroy the nerve gas and erase the computer formula. Jerry hints that he's working for the local authorities, but is shocked when Doug and Paris come in. Realizing that he's been tricked, Jerry sets off a nearby alarm. Orlov and his men arrive and search the area, and find a monkey near the alarm box. They assume it set off the alarm, put it back in its cage, and leave. Once they're gone, Jim and the others emerge from the furnace in the adjoining room, where they gagged Jerry to keep him quiet.
Dana arrives at the plant and Orlov reluctantly agrees to let her interview Vazan. As she arrives at Vazan's office, Dana uses a hidden transmitter to signal Jim that she's in position. He tells Jerry that they need his help and that he'll need theirs to get out. Jerry defends his actions betraying them, saying that he was just trying to help Judy.
Willy requisitions a van and pulls up in front of the main building next to Dana's car. He fakes a flat and then gets out of the van, goes behind it to Dana's car, and removes a collapsible filing cabinet from her car's undercarriage. Once he has it, Willy drives off.
Dana starts interviewing Vazan while a suspicious Orlov watches.
Back in the autopsy room, Paris creates a Vazan mask while Willy brings in the collapsible filing cabinet and starts assembling. An incredulous Jerry insists that they can't possibly succeed and wonders why they're going to all the effort. A disgusted Paris tells him that regardless of the nerve gas, they have a friend nearby who is twenty minutes away from death if they don't get to him in time.
When Orlov objects to the length of the interview, Dana suggests that he leave and Vazan agrees. Once they're alone, Dana gets close enough to hit Vazan with a drugged needle ring and then signals Jim. Paris dons the Vazan disguise and gets into the file cabinet, and Willy takes him out. Jerry doesn't believe that Paris' mask will fool anyone but Jim says that they're out of alternatives.
Willy takes the cabinet to Vazan's office, drops off Paris, and takes out the unconscious Vazan. As Paris calls to tell the security guard to let Willy into the autopsy room, Orlov comes back and Dana finishes her interview. In the autopsy room, Jim and Doug remove Vazan from the cabinet and Jerry assumes that Paris failed until they tell him that it's the real Vazan.
Orlov and the disguised Paris go to see Barney, who is on the verge of death. As Paris examines Barney's vital signs using a penlight, he slips a transmitter into Barney's ear. The penlight is a signal device and Paris lets Jim know that the transmitter is in position. Jim then tells Barney that Paris is Vazan and that he is to confess that two technicians, including Tirkin, helped him infiltrate the plant. Barney tells Orlov that the technicians helped him and then collapses, and Paris confirms that he's dead and sends him to the autopsy room.
Orlov goes to arrest the two technicians while the guard drops Barney off. Once they're alone, Doug examines Barney and warns Jim that their teammate may not make it. He administers emergency first aid and manages to revive him, but warns that he's too weak to move. Jim tells Doug and Barney that he'll sabotage the computer.
As Orlov interrogates Tirkin and the other man, Paris demands a current programming check. The colonel has the two supposed traitors locked up and tells Paris to replace them. Paris calls Jim, who asks Jerry if he'll cooperate. When Jerry refuses, Jim goes over the programming instructions with Barney. However, Barney warns that Jim can't possibly do it, but Jim is determined to do it no matter what. Impressed, Jerry finally agrees to help and Jim reluctantly agrees. Jerry gets the programming steps from Barney and then he and Jim go to the control room. Orlov confirms their (fake) IDs and Paris confirms that they were processed before Orlov arrived.
Willy gets Vazan out to the van and leaves with Doug and Barney. Meanwhile, Paris confirms that the two traitors sabotaged the programming but that the two new men can fix the problem. Jerry starts reprogramming the computer Orlov's nose, sabotaging the manufacturing process. A technician notices problems and tries to call, but Paris takes the call and speaks for Orlov's benefit, thanking the man for his status report. The technician tries calling again and this time Orlov grabs the receiver and takes the call. As Jerry erases the formula, Jim gives a message to Paris saying it's time to split. Paris shows the message to Orlov, distracting him so that Jim can knock him out. They head for the outer door and Willy arrives to escort them out. When the security guard Willy knocked out earlier sees Willy, he starts to sound the alarm again but Willy knocks him out before he can succeed.
Everyone gets into the van and Doug drives them out, just avoiding the soldiers. Jim assures Jerry that they're going to put Vazan somewhere that he'll never be able to make Dehominant-C, and Jerry admits that he believes him... now. Down the road they meet with Dana and a waiting Judy and make their escape via a school bus.