The Impossible Mission Force (IMF) is introduced tricking a Soviet agent into revealing his contact by point man Ethan Hunt using a disguise (including a realistic mask) as his superior. Hot off this success, their leader Jim Phelps is given a new mission to stop the traitorous agent Diatlov who's already stolen part of a list revealing the names of America's non-official covert (NOC) agents. He's going to steal the second half at an embassy party in Prague, so Phelps assembles his usual team of Ethan, Phelps' wife Claire, tech man Jack Harmon, and covert operatives Sarah Davies and Hannah Williams. Before heading out, Jack shows Ethan his new invention of explosive gum.
The mission goes smoothly at first, but soon turns disastrously wrong starting with the elevator Jack is perched on activating and crushing him into the ceiling. From there, an unseen assailant shoots Phelps causing him to fall off a bridge, Claire and Hannah's car explodes as soon as they get in, and the killer also fatally stabs Sarah and Diatlov before taking the NOC list. Ethan calls the CIA about the disaster and meets with Director Eugene Kittridge, who reveals the operation was actually a sting to find a mole, after they decrypted an online message from the mysterious arms dealer Max about "Job 314." With Ethan the only survivor, as well as a huge new deposit in his bank account he can't explain, he clearly looks like the mole and is forced to use the explosive gum to escape.
Ethan goes back to the team's safehouse, and upon glancing at a Bible realizes Max's message was actually talking about a passage from the Book of Job, the code name for the mole. He spends hours sending out messages quoting the passage to pose as Job, but is interrupted by Claire, who despite Ethan's suspicions insists she was able to escape the car bomb and is now just checking in like they were supposed to. The messages get a hit, and Ethan meets with Max's agent known only as Henchman. He's taken to Max, who turns out to be an innocuous-seeming British woman, and gets in her good graces by revealing the NOC list she has is fake, and even has a tracker attached. He offers to steal the real list from CIA headquarters, in exchange for a meeting with the real Job. Claire insists on joining him for revenge, and he recruits two other disavowed IMF agents, hacker Luther Stickell and pilot Franz Krieger.
The room with the NOC list is the most secure in the building, requiring a highly complex heist. Luther hacks into the system to create a fire alarm, allowing the others to get in posing as firefighters. After a tense moment where Ethan has to stop Krieger from stabbing an agent who catches them, Claire drugs and puts a tracker on the man assigned to the room, while Ethan and Krieger enter through the air vent. Despite some hair-raising issues involving the room's sound and pressure safeguards, the mission ends up successful and the team goes to London for the meeting with Max.
At the London safehouse, Ethan again uses a Bible quote to contact Max, but then notices the Bible is from the hotel where Phelps had said he'd be staying next. He gives the NOC list to Luther for safekeeping, then sees a news report that Kittridge has framed his mother and uncle as drug lords. After confronting Kittridge about it on a pay phone to make sure he'll come to the exchange, Ethan is approached by the still living Phelps, who claims Kittridge is the one who shot him. However, Ethan then realizes the knife he stopped Krieger from using was the same one he found with Sarah's body, and along with the Bible puts the rest together: Phelps himself is Job, and killed Jack and faked his own shooting while Krieger took out Sarah and Diatlov, though he's still unsure whether Phelps also killed Hannah or if Claire really was involved. He keeps up the act of being fooled and tells Phelps about the meeting with Max the next day on a train to Paris.
Ethan has the NOC list put under Max's seat on the train, but with Luther nearby jamming her computer before she can transmit it. Kittridge leads a team into the car, and Claire approaches Phelps in the baggage compartment, talking about how she was indeed part of the scheme. Then it turns out she was actually talking to Ethan wearing another mask, only for the real Phelps to arrive. Ethan sends a picture of Phelps to Kittridge with more IMF gear to prove he's still alive, at which Phelps kills Claire as a distraction to climb onto the roof of the train for Krieger to pick him up in a helicopter. Ethan follows and attaches the helicopter to the train, forcing Krieger to follow them into the Chunnel, and after Phelps jumps onto the helicopter he uses more of the explosive gum to blow them both up. Back on the train, Kittridge arrests Max.
With the truth proven, Luther is allowed back into IMF, but Ethan says he's decided not to. However, he's actually been made the new leader of the department, and approached with a new mission the same way Phelps used to be.
