Hunter is a former MI6 agent who lost his right eye in during a mission. Three years after the incident he is paired with James Bond in a training assigment which he fails, he is fired from MI6 for "reckless brutality" and soon receives an offer by Bond's previously deceased enemy Auric Goldfinger, a member of OCTOPUS (read: SPECTRE) to join his evil organization. Jonathan accepts the offer and now must eliminate Goldfinger's rival Dr. No, who was responsible for the injury which cost Hunter his eye in the first place, and started him on the path to evil. To help him achieve his goal he is given a gold cybernetic eye created by the equally dead Francisco Scaramanga (who is also part of Goldfinger's organization), for which he receives the codename "GoldenEye".
During his mission GoldenEye meets several villains from the 007 universe including Xenia Onatopp, Pussy Galore, Oddjob and Ernst Stavro Blofeld.