IMF agent Trevor Hanaway is killed in Budapest by assassin Sabine Moreau, who steals Russian nuclear launch codes for a man named “Cobalt”. IMF agent Ethan Hunt is extracted from a Moscow prison along with an asset named Bogdan by Hanaway’s handler Jane Carter and new field agent Benji Dunn. The team is ordered to infiltrate the Kremlin to gather information on Cobalt. However, their cover is blown, and a bomb destroys the Kremlin, leading to Ethan being blamed for the bombing and arrested by SVR agent Anatoly Sidorov. Ethan escapes and meets the IMF Secretary, who, before being killed, orders Ethan to continue pursuing Cobalt.

Ethan and analyst William Brandt identify Cobalt as Kurt Hendricks, who aims to start a nuclear war between the U.S. and Russia. The team determines Hendricks bombed the Kremlin to steal a Russian launch control device. Disavowed by the U.S. government under “Ghost Protocol”, Ethan, Brandt, Jane, and Benji plan to intercept the launch codes at a meeting in Dubai’s Burj Khalifa. They create a ruse involving posing as different individuals to fake two meetings, but things go awry, leading to a confrontation where Jane kills Moreau after a failed escape attempt. Ethan chases Wistrom, who is revealed to be Hendricks in disguise, but Hendricks escapes during a sandstorm.

The team discovers Hendricks plans to launch a missile using a Soviet satellite owned by Indian media tycoon Brij Nath. Ethan, with help from Bogdan and arms dealer The Fog, tracks the satellite and heads to Mumbai. There, Jane seduces Nath to get the satellite’s override code, while the team pursues Hendricks and Wistrom at Nath’s broadcast station. Hendricks sends launch orders to a Russian submarine to fire a missile at San Francisco. While Benji, Brandt, and Jane attempt to repair the station, Ethan pursues Hendricks, who jumps to his death to place the launch device out of reach. Benji kills Wistrom, and Ethan retrieves the launch device, disabling the missile just in time.

In Seattle, Ethan assembles his team for a new mission from Luther Stickell. Brandt confesses to Ethan about his failure to protect Ethan’s wife, Julia. Ethan reveals that Julia is alive, and her death was staged to protect her, allowing Ethan to infiltrate the prison to find Bogdan. Brandt, relieved, accepts his mission. Julia smiles at Ethan from afar, and Ethan slips away to receive an IMF debriefing, ready for the next mission.