In 1986, at Arkhangelsk, MI6 agents James Bond and Alec Trevelyan infiltrate a Soviet chemical weapons facility and plant explosives. Trevelyan is captured and executed by Colonel Arkady Grigorovich Ourumov, but Bond flees as the facility explodes.
Nine years later, in Monte Carlo, Bond follows Xenia Onatopp, a member of the Janus crime syndicate, who has formed a suspicious relationship with Charles Farrel, a Canadian Navy admiral. As Onatopp crushes the admiral to death with her thighs during sex, his credentials are stolen by Ourumov, who uses them to board a French Navy destroyer with Onatopp to steal a Eurocopter Tiger helicopter. Ourumov and Onatopp later fly the helicopter to a bunker in Severnaya, Siberia, where they massacre the staff and steal the control disk for the GoldenEye satellites, two Soviet electromagnetic pulse weapon satellites from the Cold War. They program the first GoldenEye (Petya) to destroy the complex, and escape with programmer Boris Grishenko. Natalya Simonova, the lone survivor, contacts Boris and arranges to meet him in Saint Petersburg, where he betrays her to Janus.
In London, M assigns Bond to investigate the attack. He flies to Saint Petersburg to meet CIA operative Jack Wade, who suggests that Bond meet with Valentin Zukovsky, a former KGB agent and business rival of Janus. Zukovsky arranges a meeting between Bond and Janus. Onatopp surprises Bond at the Grand Hotel Europe and attempts to kill him, but he overpowers her. She takes Bond to Janus, who reveals himself as Trevelyan; he faked his death at Arkhangelsk but was badly scarred by the explosion. A descendant of the Cossack clans who collaborated with the Nazi forces in the Second World War, Trevelyan had vowed revenge against the British after they betrayed the Cossacks, which drove his father to kill Trevelyan's mother and himself. Just as Bond is about to shoot Trevelyan, Bond is shot with a tranquilizer dart.
Bond awakens, tied up with Natalya in the helicopter, which has been programmed to self-destruct. They escape but are captured and transported to the Russian military archives, where Minister of Defence Dimitri Mishkin interrogates them. Just as Natalya reveals the existence of a second satellite and Ourumov's involvement in the Siberian massacre, Ourumov arrives and kills Mishkin. Intending to frame Bond for the murder, he calls the guards, but Bond and Natalya escape. In the ensuing firefight, Natalya is captured. Bond steals a tank and pursues Ourumov through St. Petersburg to Trevelyan's train, where he kills Ourumov. Trevelyan escapes and locks Bond in the train with Natalya, setting it to self-destruct. As Bond cuts through the floor with his laser watch, Natalya triangulates Grishenko's satellite dish to Cuba. The two escape just before the train explodes.
Bond and Natalya meet Wade in the Florida Keys and borrow his plane for the trip to Cuba, where the same night, they make love. The next day, while searching for GoldenEye's satellite dish, they are shot down. Onatopp rappels down from a helicopter and attacks Bond. After a fight ensues, Bond shoots down the helicopter, which snares Onatopp and crushes her to death against a tree. Bond and Natalya watch water draining out of a lake, uncovering the satellite dish. They infiltrate the control station, and Bond is captured. Trevelyan reveals his plan to rob the Bank of England before erasing all of its financial records with the second GoldenEye (Misha), concealing the theft and destroying Britain's economy.
Natalya programs the satellite to initiate atmospheric re-entry and destroy itself. As Trevelyan captures Natalya and orders Grishenko to save the satellite, Grishenko unwittingly triggers an explosion with Bond's pen grenade (received earlier from Q), which allows Bond to escape to the antenna cradle. Bond sabotages the antenna, preventing Grishenko from regaining control of the satellite. Bond and Trevelyan fight on the antenna's suspended platform, which finishes with Bond holding a dangling Trevelyan by his foot. Bond releases Trevelyan, who plummets into the dish. Seconds later the cradle explodes, killing Trevelyan and Grishenko. Natalya commandeers a helicopter and rescues Bond. It drops them in a field, where the couple are rescued by Wade and a team of Marines.