At the start of the game, a recording by M (head of MI6) reveals that: "Three years ago, while on assignment, the agent was severely wounded in an encounter with Dr. No and subsequently lost the use of his right eye. Consumed with vengeance, he frequently resorts to violence and brutality, and is no longer fit for service with MI6." According to the account, Dr. No shot the agent in his right eye during a mission.
Three years after the incident that claimed the agent's right eye, he is evaluated through a holographic simulation in which he is paired with 007 to stop Auric Goldfinger, a member of a criminal organization, from detonating a suitcase nuke inside Fort Knox. He fails the test and is held directly responsible for the "death" of 007. Charged with "reckless brutality," he is dismissed from MI6. As he leaves the headquarters, he is seen reading an offer by Goldfinger to enlist in his organization.
The agent accepts Goldfinger's offer and is recruited as his enforcer, meeting with him at Auric Enterprises, where Goldfinger's scientists have developed a weapon known as the OMEN (Organic Mass Energy Neutralizer), which releases energy capable of breaking down organic matter on a nearly atomic level, resulting in disintegration. For his job of eliminating Dr. No, a fellow official of the criminal organization who has declared war on Goldfinger's branch of the organization, he is given a gold-hued cybernetic eye created by Francisco Scaramanga, another official of Goldfinger's organization (from which he receives his codename "GoldenEye"). Scaramanga provides upgrades for the eye, starting with MRI vision. At Hong Kong, GoldenEye has to get a sniper rifle to take down Dr. No with the EM hack feature. At the Midas Casino, GoldenEye has to get to the vault (which can be found in multiplayer) to protect the OMEN with the magnetic polarity shield. At the Hoover Dam, GoldenEye has to destroy the dam and kill Xenia Onatopp. GoldenEye also tosses Oddjob over a rail into a pit inside the Hoover Dam after he betrays and attacks GoldenEye for unknown reasons. At The Octopus, GoldenEye has to download the navigation coordinates to Crab Key (Dr. No's base) with the help of the generated force field from his golden eye. He is eventually sent to Crab Key, where he confronts Dr. No. During their duel, GoldenEye uses his mechanical eye to sabotage the island's nuclear reactor, causing it to electrocute Dr. No. Upon No's death, Goldfinger contacts GoldenEye and informs him that he believes he is too dangerous to be left alive, and that he had contacted GoldenEye earlier and told him to activate a program which would shut down the Lair's defense grid. Goldfinger reveals that he is intent on taking over the Lair, and leaves GoldenEye to die in the impending nuclear meltdown. GoldenEye, however, manages to escape in Dr. No's osprey before the reactor overloads and the island is destroyed in a large explosion.
GoldenEye returns to the Lair intent on confronting Goldfinger. Pussy Galore rendezvous with GoldenEye and informs him that Goldfinger has used the OMEN to wipe out most of the Lair's guards, and taken control of it. Scaramanga provides the mechanical eye with a computer virus that he can use to overload the OMEN.
GoldenEye fights his way through the Lair, implanting the computer virus in the process, eventually reaching the area where Goldfinger and the OMEN are. Goldfinger traps GoldenEye inside a chamber that he claims will soon be devoid of oxygen. The computer virus then activates the OMEN, causing it to explode in a burst of energy, killing Goldfinger and his troops. GoldenEye and Galore leave the Lair aboard Galore's chopper, and Scaramanga and Number One (Ernst Stavro Blofeld) later discuss what to do with GoldenEye and decide to simply see what he does next before proceeding.