Andreas Solowiechek, a member of a Communist trade delegation, is arrested after assassinating a U.S. Senator, Townsend. Townsend's backer, McMillan, is rallying his supporters for the U.S. to break off all trade talks with the Russians. It is believed Solowiechek wasn't working on the orders of his government, so the IMF team have to break him. Rollin becomes the assassin's cellmate, and arranges to be handcuffed to him. Rollin then fakes an escape, and threatens to kill Solowiechek. The assassin promises that his backer can Rollin money. Meanwhile, Dan has pretended to be an artist and got into McMillan's house, leaving a camera behind hidden in his art box. Rollin and Solowiechek confront McMillan, and the latter admits that he arranged for Townsend to be killed so as to become a martyr to his cause, unaware that his words are being transmitted on national TV.

Dr. Erich Rojak and his wife Anna are being held in an underground laboratory/bunker by a totalitarian enemy government. Another unfriendly government has sent an assassin, Ventlos, to kill Rojak. The IMF must rescue Rojak and his wife, destroy the test missile Rojak is working on, and stop Ventlos. The IMF infiltrate the base and Jim introduces a handstamp system, unaware that Ventlos has already replaced the bunker's security chief. Jim uses his system to expose security officer Cinnamon as a phony and she is imprisoned near Anna. Willy breaks in via the furnace and rescues Anna while Cinnamon takes her place...

With Cinnamon-as-Anna in place, she is taken to her ""husband"" and tells Dr. Rojak to be near an air vent. Jim as a security officer has placed a small remote-control flying disk in the bunker's air vent system and it holds a hypo. Barney steers it to Rojak's monitored cell and he uses the hypo to induce a heart attack. Jim summons Rollin (as a heart specialist) who advises surgery and instructs that ""Anna"" be at her husband's side. Ventlos the assassin plans to disrupt the operation by taking Rollin's place in disguise and the IMF quickly has to readjust when Ventlos tries to kill Rojak and destroy the installation.

Jim and a female agent pose as scientists who have invented a new drug in order to replace a real drug that turns people into willing slaves.

As Barney taints the water system with a mind-numbing drug, Jim is captured and put on trial, where he must discredit an enemy scientist.

James Read, an enemy agent, is posing as an analyst to get to a top-secret U.S. missile guidance system being tested and steal the plans - the IMF must have him take back fake plans and unwittingly pass on the incorrect information to his superiors. Dana takes the place of Read's contact and he and fake boss Jim fake a romantic relationship so Read can get blackmail photos and use them to turn over the system. Read tells Dana of his plan to kill Jim, but before she can warn Jim, Dana is kidnapped by Hecker, a psychopath who believes Dana is a former girlfriend he killed. After Willy saves Barney from a firetrap meant for Jim, Paris and Barney manage to rescue Dana and alert Jim just in time to avoid a rigged car, convincing Read he's in the clear with the guidance system.