Ethan Hunt, an IMF operative, is broken out of a Russian prison by his team and tasked with infiltrating the Kremlin to obtain information regarding a terrorist named Cobalt. During the mission, however, the team is framed for the bombing of the Kremlin, leading to the President initiating "Ghost Protocol", a black-ops contingency that disavows the entire IMF. Hunt and his team, including tech wizard Benji and intelligence analyst William Brandt, are left without any support or official ties to the U.S. government. They must rely solely on their skills and wits to pursue Cobalt and clear their organization's name.

In order to track down Cobalt and prevent a potential nuclear conflict, Hunt's team follows a trail of clues leading them across the globe. From a vertiginous mission scaling the world's tallest building in Dubai to a covert infiltration in Mumbai, they draw upon their individual talents and improvised gadgets in the face of escalating challenges. As they close in on the terrorist's plot, personal stakes heighten tensions within the team, exposing secrets that could jeopardize their mission and their lives.