The game opens with a recording from M, head of MI6, explaining that three years earlier the agent was gravely wounded by Dr. No during a mission and lost the use of his right eye. Consumed by a thirst for vengeance, he has grown brutal and violent, no longer fit to serve.
Three years on, the agent is tested in a holographic simulation alongside 007, the two tasked with stopping Auric Goldfinger from detonating a suitcase nuke inside Fort Knox. He fails, is blamed for 007's "death," and — charged with reckless brutality — is dismissed from MI6. On his way out, he's reading an offer from Goldfinger to join his organization.
The agent accepts and becomes Goldfinger's enforcer at Auric Enterprises, where scientists have built the OMEN (Organic Mass Energy Neutralizer), a weapon that breaks down organic matter at nearly the atomic level, disintegrating it. To carry out his job of eliminating Dr. No — a rival official who has declared war on Goldfinger's faction — he's given a gold cybernetic eye made by Francisco Scaramanga, which earns him the codename "GoldenEye." Scaramanga supplies upgrades for it, beginning with MRI vision. Across his missions he acquires a sniper rifle to take down Dr. No in Hong Kong using the EM hack feature, reaches the vault at the Midas Casino to protect the OMEN with a magnetic polarity shield, destroys the Hoover Dam and kills Xenia Onatopp, and tosses Oddjob into a pit there after Oddjob betrays him. At The Octopus he uses his eye's force field to download navigation coordinates to Crab Key, Dr. No's base.
On Crab Key, GoldenEye confronts Dr. No and sabotages the island's nuclear reactor with his mechanical eye, electrocuting him. With No dead, Goldfinger contacts GoldenEye, declares him too dangerous to live, and reveals he'd earlier tricked him into shutting down the lair's defense grid so he could seize it — then leaves GoldenEye to die in the meltdown. GoldenEye escapes in Dr. No's osprey just before the island is obliterated.
Determined to confront Goldfinger, GoldenEye returns to the Lair. Pussy Galore meets him and warns that Goldfinger has used the OMEN to wipe out most of the guards and taken control. Scaramanga arms the mechanical eye with a virus to overload the OMEN. Fighting through the Lair and planting the virus, GoldenEye reaches Goldfinger, who seals him in a chamber meant to suffocate him. The virus then triggers the OMEN, which erupts in a burst of energy that kills Goldfinger and his troops. GoldenEye and Galore flee by chopper, while Scaramanga and Number One (Ernst Stavro Blofeld) decide to watch what GoldenEye does next before acting.