A government scientist, Paul Morse, plans to sell a biological weapon, TOD-5, to terrorist Alpha Group led by Dr. Flory. The IMF must get to Morse's contact, Gordon Holt, and get him to take them to Alpha HQ. When Holt gets to the small town where he is to get the weapon from Morse, he finds the town under quarantine and people dying - then he starts showing (IMF-faked) symptoms of the disease. He grabs Mimi, who is supposedly immune, and takes her with him to Alpha HQ and infects them to force them to come up with an antidote - the IMF trail him and arrest the whole operation.

L'équipe de Mission Impossible convainc Gordon Holt, un agent double, qu'il a été contaminé lors de la livraison à un groupe de terroristes d'une arme biologique volée. Après avoir enfin localisé leur repaire, l'agent Mimi Davies se fait passer pour la petite amie de Holt.