克里姆林宮發生了恐怖襲擊，而總統已經接受了“幽靈協議。湯姆克魯斯飾演的伊森等·亨諸特身處危機險境，將被帶到華盛頓為克林姆林宮爆炸案接受起訴。一旦如果被抓住，將會成為開啟世界核戰爭的恐怖分子。而他手下由傑瑞米·雷納、西蒙·佩吉組成的團隊也不平靜。
 
When a terrorist bombing destroys the Kremlin, the United States government initiates a black ops "ghost protocol" and disavows the entire Impossible Mission Force. Ethan Hunt and his team are to be blamed for the attack, but are allowed to escape as part of a plan to enable them to operate in the dark, outside of their agency. However, Hunt is warned that if any member of his team is captured during their mission, they will be charged as terrorists planning to incite global nuclear war. Ethan is then forced to work with ex-IMF agent Brandt, who knows more about Hunt and his past than even Hunt himself.