Lorsque deux bombes atomiques sont dérobées par le SPECTRE, James Bond est mandaté par le gouvernement britannique pour retrouver les bombes. Pour ce faire, il devra se rapprocher du No 2 de l'organisation criminelle, Emilio Largo. Aidé par le MI6 ainsi que par son fidèle allié Felix Leiter, de la CIA, Bond devra patrouiller les fonds marins des Bahamas afin de retrouver la trace des bombes manquantes.
In Istanbul the MI6 agents James Bond and Eve chase a mercenary, Patrice, who has stolen a computer hard drive containing details of undercover agents placed in terrorist organisations by NATO states. Patrice wounds Bond in the shoulder and, as the two men fight atop a train, M, the head of MI6, orders Eve to fire a distant shot with a rifle at Patrice; Eve misses and inadvertently shoots Bond, allowing Patrice to escape. Bond falls into a river and goes missing, presumed to be dead.
On a mission in Mexico, unofficially ordered by the previous M, James Bond kills two men arranging to blow up a stadium; in doing so the building they are in explodes and collapses. Bond gives chase to Marco Sciarra, who survived the blast; Sciarra boards a helicopter to escape. Bond follows and in the ensuing struggle he throws both Sciarra and the pilot out of the helicopter, stealing Sciarra's octopus ring as he does so. On his return to London Bond is indefinitely taken off field duty by the current M, who is in the midst of a power struggle with C, the head of the Joint Intelligence Service, which consists of the recently merged MI5 and MI6. C also wants to create the "Nine Eyes" intelligence co-operation agreement between nine countries, and close down the '00' section in the process.
Ethan Hunt accepte une nouvelle mission décrite sur une bande magnétique qui s'autodétruit cinq secondes plus tard : le « Syndicat », dont le chef, Solomon Lane, a été arrêté deux ans auparavant par Hunt et son équipe, s'est reformé sous la forme d'un groupe terroriste dénommé « Les Apôtres », avec l'aide de Nils Debruuk, spécialiste norvégien en armes nucléaires. La mission de Hunt est d'intercepter une livraison de trois charges portables de plutonium aux Apôtres, qui doit se dérouler à Berlin. Il s'y rend avec Benji et Luther, mais ce dernier est pris en otage par les Apôtres ; en voulant le sauver, Hunt oublie de surveiller les bombes dont s'emparent les terroristes.
In Budapest to intercept a courier working for an individual code-named "Cobalt", IMF agent Trevor Hanaway is killed by assassin Sabine Moreau. Hanaway's team leader, Jane Carter, and newly promoted field agent Benji Dunn extract Ethan Hunt and his source, Bogdan, from a Moscow prison. Ethan is recruited to lead Jane and Benji to infiltrate secret Moscow Kremlin archives and locate files identifying Cobalt. During the mission, someone broadcasts across the IMF frequency, alerting the Russians to Ethan's team. Although Benji and Jane escape, a bomb destroys the Kremlin and SVR agent Anatoly Sidorov arrests Ethan, suspecting him as a key player in the attack.
After intercepting nerve gas being sold to terrorists, Impossible Missions Force (IMF) agent Ethan Hunt (Tom Cruise) is convinced he can prove the existence of the Syndicate, an international criminal consortium that the Central Intelligence Agency (CIA) does not believe exists. Hunt is captured by the Syndicate, but escapes a torture chamber led by Syndicate member Janik "Bone Doctor" Vinter (Jens Hultén) with the help of MI6 agent and Syndicate operative Ilsa Faust (Rebecca Ferguson).
After killing Dryden, a traitorous MI6 section chief—who has been selling classified information—and the chief's contact, James Bond receives his double-0 status and is designated 007. He then travels to Madagascar in pursuit of Mollaka, a globe-trotting bombmaker-for-hire. After a parkour chase to an unnamed African embassy, Bond kills Mollaka against orders and escapes by setting off an explosion which immobilizes the embassy's security forces. Searching through Mollaka's mobile phone, Bond discovers a text message, which he traces to Alex Dimitrios, an associate of the banker and terrorist financier Le Chiffre. Aided by Mr. White, who is a representative of a terrorist organization later revealed to be Quantum, Le Chiffre is introduced to Steven Obanno, a high ranking member of the Lord's Resistance Army in Uganda, and arranges to bank several briefcases full of cash for Obanno. Le Chiffre, however, decides to invest the money into stock in a successful company called SkyFleet and then engineers a terrorist attack to sink its share prices, creating huge profits for himself.
James Bond is driving from Lake Garda to Siena, Italy, with the captured Mr. White in the boot of his car. After evading pursuers, Bond and M interrogate White regarding his organization, Quantum. M's bodyguard Craig Mitchell, a double agent, attacks M, enabling White to escape. Bond chases Mitchell and kills him. Bond and M return to London and search Mitchell's flat, discovering through tagged banknotes that Mitchell had a contact in Haiti. Bond tracks the contact, Edmund Slate, and learns that Slate is a hitman sent to kill Camille Montes at the behest of her lover, environmentalist Dominic Greene. While observing her subsequent meeting with Greene, Bond learns that Greene is helping an exiled Bolivian General, Medrano—who murdered Camille's family—to overthrow his government and become the new president in exchange for a seemingly barren piece of desert.
Ethan Hunt (Tom Cruise), while vacationing, is alerted by the IMF that someone has used his identity to assist Russian bio-chemical expert Dr. Vladimir Nekhorvich (Rade Serbedzija) of Biocyte Pharmaceuticals to enter the United States, only to kill him in a subsequent plane crash. Nekhorvich, an old friend of Ethan, had forewarned the IMF of his arrival, planning to deliver a new bioweapon, Chimera, and its cure, Bellerophon, both of which he was forced to develop by Biocyte, into the IMF's hands. With his death, IMF is worried that the virus is out in the open, believing that rogue IMF agent Sean Ambrose (Dougray Scott) is responsible. IMF assigns Ethan to recover it. Ethan is told that he can use two members of his team to help him, but the third person to help him must be Nyah Nordoff-Hall (Thandie Newton), a professional thief presently operating in Seville, Spain, as she will be able to get close to Ambrose, being an ex-girlfriend.
The film opens with construction executive John (Brad Pitt) and tech support representative Jane Smith (Angelina Jolie) answering questions during marriage counselling. The couple has been married for "five or six" years, but their marriage is suffering to the point that they cannot remember the last time they had sex. They tell the story of their first meeting in Bogotá, Colombia, where they were both secretly on the run from the Colombian authorities - since the authorities were looking for tourists travelling alone after a recent heist, the two claimed to be together to avoid being questioned. They quickly fell in love and married. John later states that Jane "looked like Christmas morning" to him on the day they met.
Several years after the events of the series, Jim Phelps (Jon Voight) and his team, the Impossible Mission Force, are assigned to retrieve the IMF non-official cover list from the American embassy in Prague. Their mission fails: Phelps is shot point blank, his wife Claire (Emmanuelle Beart) dies in a car bombing, and the rest of the team except agent Ethan Hunt (Tom Cruise) are eliminated by an unknown assassin. Meeting later with IMF director Eugene Kittridge (Henry Czerny), Hunt learns the job was a setup designed to lure out a mole within IMF, whom IMF believes to be in contact with an arms dealer known as "Max" as part of "Job 314." As Hunt is the only member left, Kittridge suspects him of being the mole, and Hunt flees.
Following his pursuit by Kirill, Jason Bourne (Matt Damon) evades Moscow police. Six weeks later, CIA Deputy Director Pamela Landy (Joan Allen) divulges the audiotaped confession of Ward Abbott, the late former head of Operation Treadstone, to Director Ezra Kramer (Scott Glenn). Meanwhile, in Turin, journalist Simon Ross (Paddy Considine) of The Guardian meets an informant to learn about Jason and Operation Blackbriar, the program succeeding Treadstone. The CIA tracks Ross as he returns to London, after his mention of "Blackbriar" during a cell-phone call to his editor is detected by the ECHELON system. Jason reappears in Paris to inform Martin Kreutz (Daniel Brühl), the step-brother of his girlfriend Marie Helena Kreutz (Franka Potente) of her assassination in India.
James Bond infiltrates a North Korean military base, where Colonel Tan-Sun Moon is illegally trading weapons for African conflict diamonds. After Moon's assistant Zao discovers that Bond is a British agent, the colonel attempts to kill Bond and a hovercraft chase ensues, which ends with Moon's apparent death. Bond survives, but is captured by North Korean soldiers and imprisoned by the Colonel's father, General Moon.