After intercepting nerve gas being sold to Chechen terrorists in Minsk, IMF agent Ethan Hunt is convinced he can prove the existence of the Syndicate, an international criminal consortium that the CIA does not believe exists. Hunt is captured by the Syndicate, but escapes a torture chamber led by Syndicate member Janik “Bone Doctor” Vinter with the help of disavowed MI6 agent and Syndicate operative Ilsa Faust.
CIA Director Alan Hunley and IMF Field Operations Director William Brandt testify before a Senate committee. The IMF, currently without a secretary in charge, is controversial because of its destructive methods and various misconducts. Hunley succeeds in having the IMF disbanded and absorbed into the CIA. Brandt, knowing that Hunley will try to capture Hunt, warns him to stay undercover. Cut off from the IMF, Hunt follows his only lead: a blonde man in glasses, later identified as former MI6 agent Solomon Lane.
Six months later, Hunt remains a fugitive. He enlists former colleague Benji Dunn to attend an opera in Vienna. He predicts that an attempt will be made on the Austrian Chancellor at the performance, and believes that Lane will also be there. He and Dunn stop three snipers including Faust, but the Chancellor is killed by a car bomb, and Lane is still not found. Faust drops hints of Lane’s plan to Hunt before leaving. Dunn decides to stay with Hunt instead of reporting back to the CIA, despite knowing his action amounts to treason.
Hunt, blamed for the Chancellor’s death, is pursued by the CIA’s Special Activities Division. Brandt contacts Luther Stickell to find Hunt before the CIA does. Stickell tracks Hunt, Dunn, and Faust to Casablanca. Here, they acquire a list of Syndicate agents, contained in a secure building. Faust flees with the data, evading both Hunt and Syndicate members, although Hunt kills the pursuing Syndicate members. Dunn reveals he copied the data onto a USB drive, as Stickell and Brandt catch up to them.
Faust returns to London and attempts to use the file to quit her mission to infiltrate the Syndicate, but her MI6 handler, Atlee, compels her to continue, whilst discreetly wiping the drive. Meanwhile, Ethan learns that the data is actually an encrypted British-government red box that requires the Prime Minister’s biometrics to unlock it. Lane’s men abduct Dunn, and use Dunn and Faust to blackmail Hunt into decrypting the data and delivering it to them. Hunt agrees to the ultimatum, despite protests from Brandt.