In Mexico, James Bond (Daniel Craig) assassinates corrupt businessman Marco Sciarra and retrieves his ring, bearing the symbol of an octopus, before returning to London, where he is reprimanded by M (Ralph Fiennes) for his recklessness. Bond notices there's surveillance cameras in the new office. Intelligence official Bruce Denbigh (Andrew Scott), also known as "C", is advocating for England's secret services to be merged under one program codenamed "Nine Eyes", scrapping the 00 Section in the process, and Bond's actions have led credence to his campaign. A vote to decide the approval of Nine Eyes is to held in Tokyo in a few days.
Eve Moneypenny (Naomie Harris) visits Bond in his apartment to give him a box of his belongings from Skyfall Manor, among them a picture of Bond with his foster family and a message left by M (Judi Dench) revealing evidence that Sciarra was a member of a mysterious organization behind a series of terrorist attacks across the globe. Bond convinces Moneypenny to help him stop them.
The following day, Bond and Bill Tanner (Rory Kinnear) visit the Q-Branch underneath the abandoned MI6 office at Whitehall, which is scheduled for demolition. Q (Ben Whishaw) injects Bond with a nanotechnological device that allows MI6 to trace him through his blood on M's behalf. Q gives Bond 48h to pursue his lead on the organization, while M is in Tokyo for the Nine Eyes summit. Bond gives Moneypenny a cellphone to keep in contact, steals a modified Aston Martin DB-10 and travels to Rome, where he attends Sciarra's funeral and seduces his widow, Lucia Sciarra (Monica Belucci), into giving him the password to a meeting between the leaders of SPECTRE, led by Franz Oberhauser (Christoph Waltz). Oberhauser mentions "The Pale King" in Mondsee, Austria, before spotting Bond, who flees.
While being chased by Oberhauser's enforcer, Hinx (Dave Bautista), Bond contacts Moneypenny, who identifies the "Pale King" as Mr. White (Jesper Christensen), a former Quantum member who lives in Mondsee. Bond evades Hinx and heads there, while in Tokyo, all present countries vote in favor of Nine Eyes except for South Africa. M points out the vote has to be unnanimous, but C is certain that Nine Eyes will be approved. M learns that Bond has gone rogue and Q travels to Austria to warn Bond. M informs Moneypenny that Bond's actions have further damaged MI6's reputation.
Bond arrives at Mr. White's estate and finds him dying after Oberhauser has decided to disavow him. Mr. White bargains for Bond to protect his daughter, Madeline Swann (Lea Seydoux), in exchange for Swann leading him to the L'American Hotel where he'll find information about Oberhauser. Hinx finds out Bond is going after Madeline. Bond meets Q at the secluded health clinic for the wealthy where Madeline works and gives him Sciarra's ring before approaching Madeline, who is then kidnapped by Hinx and his men. Bond rescues her and they return to Q's hotel, where Q learns from a data storaging device embedded in Sciarra's ring that he was a member of SPECTRE, which has bankrolled Quantum and is behind Le Chiffre, Dominic Greene and Raoul Silva. Reports come in of a bombing in South Africa that has led the government to reconsider their stance on Nine Eyes. The program is approved, with C as its commander, and M and his employees, including Moneypenny and Q, are fired.
Bond and Madeline arrive at the L'American and flirt. Bond finds a secret room belonging to Mr. White, who had been assigned by Oberhauser to a series of operations that affected Bond directly, tipping Bond to Oberhauser's true identity. Bond finds a map to Oberhauser's hideout in Sahara. Bond and Madeline board a train to Tangier, where Bond is attacked by Hinx, who ends up being killed. Bond and Madeline have sex and fall in love.
In Tangier, Bond and Madeline are welcomed by Oberhauser's butler, who drives them to his state in Sahara. Bond recognizes Oberhauser as his foster brother, who murdered his father out of jealousy for believing he favored Bond. Oberhauser controls a network of spy-satellites that allows him to monitor the entire planet through surveillance cameras, including MI6, and mastermind terrorist attacks for profit.
Bond and Madeline escape and reach Oberhauser's control center. Bond contacts Q, who teaches him how to sabotage it, leading to an explosion that destroys Oberhauser's estate. Bond and Madeline return to London with evidence that C was in league with Oberhauser and M agrees to help them despite MI6 having already been decommissioned. Bond the infiltrates C's office and attempts to arrest him, but C draws a gun, forcing Bond to kill him.
Suddenly, Oberhauser, who survived albeit heavily disfigured, causes a citywide blackout to lure Bond into a final confrontation at the old MI6 office in Whitehall, which is rigged to explode in a matter of minutes. Bond infiltrates the building and kills Oberhauser's men before confronting Oberhauser underground. He reveals that Madeline is being held captive atop the building, and Bond leaves to rescue her while Oberhauser departs in a helicopter. Bond and Madeline manage to escape before the building collapses and chase after Oberhauser's helicopter, which Bond manages to shoot down with a flare. Bond confronts Oberhauser as he crawls out of the wreckage of the helicopter, but chooses to spare him, in the process addressing him by his childhood name: Ernst Stavro Blofeld.
In the aftermath, Blofeld is arrested alongside the other members of SPECTRE, Nine Eyes is decomissioned, M is reinstated as head of the MI6 and Bond and Madeline leave together to enjoy a vacation.