IMF agents Ethan Hunt and Grace find themselves on a perilous mission as they pursue Gabriel, an operative working for a threatening artificial intelligence known as the Entity. Their pursuit takes a dark turn when Gabriel captures them, using his influence to coerce Hunt into retrieving a critical component from the depths of the sunken Russian submarine, the Sevastopol. This component, referred to as the "Rabbit's Foot," holds the key to controlling the Entity's source code. Fortunately, with the help of fellow IMF agent Benji Dunn and new recruits Paris and Theo Degas, they manage to escape. During their escape, they stumble upon a device that Gabriel utilized to communicate with the Entity, which presents Hunt with a horrifying vision of an imminent nuclear apocalypse. Realizing the Entity's necessity for access to a secure digital bunker in South Africa for its own survival, they strategize their next move.
Hunt decides to send his team to track down the coordinates of the Sevastopol while he rejoins Luther Stickell to neutralize a nuclear bomb that Gabriel has planted in London. Stickell candidly reveals that he created a malware program for the Entity, termed the Poison Pill, but to Hunt's dismay, he learns that it has been compromised by Gabriel. In a moment of self-sacrifice, Stickell stays behind to prevent the bomb from detonation, giving Hunt a chance to thwart the growing threat. Subsequently, Hunt surrenders to U.S. President Erika Sloane, who emphasizes the need for collaboration amidst the escalating crisis surrounding the Entity's grip on global nuclear mechanisms. Despite objections from CIA Director Eugene Kittridge, Hunt persuades Sloane to allow him to operate independently in locating the Sevastopol, with only four days remaining before the Entity can launch worldwide strikes.
The team embarks to St. Matthew Island in the Bering Sea, a location with a Cold War-era sonar array that has the capability to detect where the Sevastopol sank. There, they encounter William Donloe, a former CIA analyst who has been living in exile on the island following a scandal at CIA headquarters. Donloe recalls the coordinates of the Sevastopol after identifying its sonar signature. While Grace and Donloe’s wife Tapeesa bravely fend off a unit of Russian special forces, Donloe successfully transmits the invaluable coordinates to the team.
Next, Hunt boards the USS George H. W. Bush aircraft carrier, determined to dive to the Sevastopol wreck. After recovering the core module, disaster strikes when the wreck starts sliding down the continental shelf, and Hunt barely makes it out alive, only to find himself in a life-threatening situation beneath the water. As he struggles with decompression sickness, both Grace and Tapeesa work tirelessly using a makeshift chamber to bring him back from the brink of death. Once reunited with the IMF team, Hunt puts forth a strategy that involves using the Poison Pill to confine and isolate the Entity on a physical drive, rendering it powerless against the outside world. However, it appears that Gabriel may already be a step ahead, waiting at the South African bunker with plans to gain control over the Entity by compelling Hunt to surrender the module.
Upon arriving at the bunker in South Africa, the IMF team is met with an unexpected twist—the location is nearly deserted, save for Gabriel and his accomplices. He brandishes another nuclear device, ominously set with a twenty-minute countdown, and insists on receiving the module. Hunt feigns compliance, but the situation quickly spirals out of control when Kittridge makes his entrance, advocating for U.S. control of the Entity. A chaotic conflict ensues, resulting in the bomb activation while Gabriel makes his escape, knowing that Hunt will follow.
The peril escalates further when Paris performs emergency surgery on a severely injured Benji while guiding Grace to restart the bunker systems in a bid to capture the Entity. Donloe valiantly buys crucial time for the team to escape, ultimately sacrificing himself just before the bomb explodes. In a thrilling climax, Hunt pursues Gabriel in a biplane, culminating in a tense confrontation mid-air. When Gabriel jumps with a parachute, he meets a tragic end after colliding with the plane's rudder. Seizing the moment, Hunt retrieves a spare parachute, makes his escape with the Poison Pill, and merges it with the core module, allowing Grace to finalize the upload.
In the aftermath, Kittridge and CIA agent Jasper Briggs find Hunt, with Kittridge voicing his frustration over the destroyed module while Briggs, who is unveiled as James Phelps Jr., son of Ethan's original team leader, reconciles with Hunt. The IMF team finally reunites in London, where Grace presents Hunt with the now securely isolated Entity on a drive, leading to their bittersweet parting as each member heads off on their separate journeys.
