General Zepke plans to rise to power - the only threat to him is Cardinal Souchek who stands for a free people. Zepke has had Souchek imprisoned and plans to replace him with a double who will endorse him. The IMF use an infected mosquito to make the doiuble, Nagorski, ill. Phelps and Cinnamon are called in as doctor and nurse to tend to him while Rollin impersonates a Cardinal and sees through Nagorski's impersonation. He escapes from an airtight sarcophagus and helps Barney and Willy enter the monastery through a booby-trapped tunnel before their air runs out. When Jim has Nagorski placed in an oxygen tent, the others open up the wall behind him, take out Nagorski and replace him with Souchek whom they've secretly freed. Zepke has Souchek-as-Nagorski-as-Souchek give a speech, but Souchek doesn't say what Zepke was expecting...

A scientist of an enemy power, Dr. Oswald Beck, has developed a bacteria which causes cerebral spinal meningitis and mutated it into a form that kills and then becomes inert after a few hours. The IMF must destroy the preliminary culture and stop Beck. Rollin replaces the prisoner chosen for a test of Beck's bacteria, and Barney switches the bacteria cylinder for one with knockout gas and then uses a balloon to capture the gas. Rollin ""dies"" but then Jim, who has infiltrated the base as a military medic, ""discovers"" that Rollin isn't dead. Meanwhile, Barney releases the knockout gas into the control room, knocking out Beck's superiors. Beck thinks they are dying from his bacteria and believes they'll think he's a traitor who tried to kill them rather than the test subject. He flees but is shot while Jim destroys the bacteria.

Gregory Tolan leads an underground cell specializing in bank robberies with the money going to finance an American revolution. His mysterious sponsor is Jonathan Brace, who runs other such cells throughout the U.S. The IMF must find out Brace's identity and apprehend him. Phelps (as a demo expert) and Dana (as his insider at Tolan's next target) get recruited and has to make sure Tolan steals the money without the police knowing so he can lead them to Brace. When Jim stops Tolan from shooting Willy (disguised as a clerk), the police are alerted and Tolan's team takes refuge. Jim goes to get a (bugged) car since Brace won't come to them, Paris and IMF guest agent Grace play the homeowners, and Dana and Tolan exit with the money when Brace orders them to. Jim stops the hostages from getting killed and they follow Tolan to Brace and bring them both in.

Berlinger, a millionaire manufacturer and stolen gem dealer, will be transferring diamond to a Syndicate boss for $75 million. Only one man knows where the diamonds are - Hoffman, Berlinger's former lieutenant, who stole them. Berlinger is torturing Hoffman for their location. The IMF must get the gems and the money. Barney springs Hoffman and they become partners so Hoffman dives for the gems (hidden on the body of a courier sunk at sea). Casey brings Berlinger to Jim, posing as a diver, who offers to get the diamonds. Willy follows Hoffman to the gems and the team knocks him out and takes him into custody - then Jim leads Berlinger to the same spot and offers to make a deal in return for his $5 million payment. Under pressure from the Syndicate, Berlinger agrees and in the subsequent meeting the police capture everyone.

Peter Cordel, a hitman and grandmaster chess player, has evaded capture - the IMF must bring him to justice and determine who in the Syndicate he works for. Using a hypnotic drug given by guest-agent Sandy, the IMF condition Cordel to blackout every time he is told ""When in doubt, take a pawn."" Then they set it up so it looks like he kills several people during his blackouts and have him awaken in a mental hospital where an IMF orderly stages an assault to make it look like Cordel's boss wants him dead, so Cordel tells Sandy to warn his boss to call off his hit men, and the IMF capture the man.