Set in between Quantum of Solace and Skyfall, MI6 Agents James Bond and Alec Trevelyan are tasked by M with infiltrating a chemical weapons facility in Arkhangelsk, Russia, which is believed to be the source of weapons used by a terrorist cell to target British embassies around the globe. The mission goes awry when Trevelyan is shot by General Ourumov. Bond escapes by detonating explosives he had placed throughout the facility before fleeing Arkhangelsk via aeroplane.

Later, a phone call intercepted from Ourumov connects him to Russian gangster Valentin Zukovsky as Ourumov attempts to acquire a helicopter that has been modified to survive an electromagnetic pulse. Zukovsky directs him to an arms fair in Dubai but is unable to stop Onatopp and Ourumov from stealing the helicopter. However, he is able to plant his smartphone on board, and MI6 is able to track the helicopter to a remote base in Siberia. Bond is unable to stop the theft of a GoldenEye weapons satellite which is detonated by Ourumov. Bond is able to rescue Natalya Simonova before being arrested by the Russian army.

Believing Bond and Simonova to be responsible for the GoldenEye blast, Russian Defense Minister Dmitri Mishkin interrogates the two in Saint Petersburg, but is killed by Ourumov, who then abducts Natalya. Bond pursues him to a train and confronts him over his plan for the GoldenEye satellite. Onatopp betrays Ourumov and kills him. Bond is able to help Natalya off the train and goes to a meeting at Statue Park learning that Trevelyan survived his execution at the hands of Ourumov and is now Janus, the mastermind behind the GoldenEye theft and leaves with Natalya, who is instrumental to his plan. Bond is able to infiltrate a solar facility in northwestern Nigeria and tricks Trevelyan into destroying his supercomputers stopping his plan to use the satellite to destroy London erasing evidence of finances he stole. After fighting Trevelyan, Bond is able to overload the facility control room and shoot Trevelyan, sending him to his death over the tower. Simonova and Bond escape the base by helicopter, with the couple kissing in the mission's aftermath.