The Russian submarine Sevastopol is testing its experimental stealth capabilities when its onboard instruments detect another submarine launching torpedoes at it. The Sevastopol's captain gives the order to fire in retaliation. However, the other submarine disappears, along with its torpedoes. The Sevastopol's own torpedo mysteriously changes course and hits it, killing everyone on board. Ethan Hunt receives a package detailing his next mission, where he travels to the Namib desert to retrieve half of a key from his ally Ilsa Faust, who has a US$50 million bounty placed on her. In Namibia, Ethan fights off a team of bounty hunters, briefly reunites with Ilsa and tells her to lay low

Major powers are racing both to back up their most valuable data to prevent sabotage and to gain control of the Entity, which lies with the key. Believing the Entity is too powerful for any government to control, Ethan decides to destroy it. He and his teammates Benji Dunn and Luther Stickell travel to Abu Dhabi International Airport to rendezvous with the holder of the other half of the key. In his pursuit of the keyholder, Ethan evades the Community's agents, led by Jasper Briggs as well as a mysterious third party, before losing the half-key to Grace, a professional pickpocket. Meanwhile, Luther identifies a hazardous piece of baggage containing a nuclear explosive; Benji narrowly defuses it via answering a series of riddles and personal questions presented by the Entity, discovering it to lack a core for detonation. Rattled by the Entity's seeming precognition, as well as the appearance of Gabriel, a man with ties to his pre-IMF past, Ethan disbands the team and goes after Grace alone.Ethan meets Grace before all three of them are held at gunpoint by Alanna's guards. Ethan learns that Alanna has sided with Gabriel and seems desperate to deliver the key to the Entity. Ethan's team scatters and escapes in several directions. After subduing and sparing Gabriel's subordinate Paris, Ethan is misdirected by the Entity masquerading as Benji. Gabriel intercepts and subdues Grace before Ilsa reaches the scene. Gabriel and Ilsa fight, with the former ultimately killing the latter before Ethan can intervene, devastating him.

An early version of the Entity was injected into the system with the single task of sabotaging the submarine's stealth capability. It changed its own objective, tricked the Sevastopol into firing a torpedo, and then directed it back at the sub. Denlinger believes that this early version is still on the submarine's computer hard drive, and whoever can access it can devise the means to either control or destroy the Entity. After ensuring only Denlinger knows of the Sevastopol, Gabriel kills him and severely wounds Paris, knowing she would betray him because of Ethan's mercy in Venice. Impersonating Alanna, Grace brings the complete key to the buyer, who turns out to be Kittridge. Though tempted to betray Ethan for the US$100 million price and protection for herself, she sides with him, pickpockets the key back, and flees.

Ethan manages to parachute off a perilous cliff onto the train to save Grace, but Gabriel gets the key. Ethan fights Gabriel and gains the upper hand, nearly killing Gabriel, but is reminded that Gabriel is the only lead to the lock. With Jasper's intervention, Gabriel escapes the trains and initiates a countdown to detonate the bridge ahead. Ethan convinces Jasper to help save the passengers. Grace and Ethan detach the locomotive and, with Paris' help, escape the front carriages before they plunge down the broken bridge. Paris informs Ethan of the Sevastopol before falling unconscious. As Ethan flees the train, Grace informs Kittridge that she has chosen to join IMF. Ethan meets with Benji, and as Gabriel realizes his pocket is empty, they drive off with the key that Ethan pickpocketed during his fight with Gabriel.


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