IMF team leader Jim Phelps picks up his briefing on an empty rooftop. Two men, Stoner and Cardel, are scientists vital to the development of a special U.S. project. They and their wives have been kidnapped by enemy agent Eric Stavak, who needs to get a third man to acquire the project formula. The IMF must prevent Stavak from getting the third scientist, and recover the other two.
In the final briefing, the team tests a vibrational device capable of shattering glass. Rollin needs to get into Stavak's headquarters to map out the area for Barney. Jim and Cinnamon are going to take the place of the third scientist and his wife, the Websters.
Rollin and Cinnamon attend the death of Mrs. Webster's mother and Cinnamon activates a tracking device in her necklace, which Barney and Willy monitor from a van. Stavak's men knock out Cinnamon's driver and substitute one of their own. Rollin and Cinnamon leave and the driver takes them to a warehouse where they are blindfolded and transferred to another vehicle. They are then taken into Stavak's headquarters where Rollin reveals he's not Webster but just Cinnamon's friend. Stavak insists that Cinnamon get her husband there but she points out he's under heavy guard. Stavak gives her one hour to consider the matter before he kills her.
Barney and Willy find the place while Cinnamon and Rollin are put in a cell with the other prisoners. Cardel's wife Emily claims not to recognize Cinnamon but the latter quickly covers until she can let hem know what's going on. Willy and Barney take pictures and measurements of the outside while Rollin makes a map of the interior. Finally Cinnamon relents and tells Stavak she wants $25,000 to betray her husband. Stavak agrees and Cinnamon calls Jim and asks him to come to her but at a different location then the one Stavak wants her to meet him at. Stavak reluctantly agrees and pays her off.
Cinnamon meets with Jim and Stavak's men take him prisoner, as Rollin and Cinnamon leave. Stavak has them followed with orders to be killed. Rollin and Cinnamon duck into a building and Willy and Barney take Stavak's man captive. Stavak tells Jim and the other scientists to release the plans and leaves them alone, while Barney tests their sonic broadcaster. Cinnamon calls the police with a report of a gas leak so they evacuate the neighborhood.
The team pretends to be workers to evacuate the area and then set up their equipment around the building. Inside, Jim wants to give up the formula but the other two scientists refuse. Jim says he has enough on his own to give Stavak what he needs. Jim prepares to write out the formula and stalls. Stavak finally catches on but before they can have him killed, the IMF activates a fake earthquake with the sonic broadcasts. Willy dumps debris down the stairs while Barney causes a gas leak.
Jim tells the scientists to play along while the police arrive, but Rollin quickly convinces them they're dealing with a gas leak. Jim points out there's a gas leak and they don't have much time, then rigs up a radio transceiver. Rollin goes on the air and sends fake broadcasts about the earthquake along with a coded message directing Jim to a fake storm drain pipe they've set up.
Jim bargains for their life in return for Stavak letting them go. Stavak agrees and Jim insists on taking their bullets, then uses the gunpowder to blow a hole in the wall. Jim and the others dig their way out. Once they're close to the surface, Stavak draws a gun and forces Jim and the scientists to stay behind while he and his men escape. Once they're gone, Jim directs the others with him to an elevator shaft providing them with a handy exit. Meanwhile Stavak emerges last and finds no signs of an earthquake, He and his men are taken into custody as the team reveal to the scientists that the gas was just as fake as the earthquake.