According to co-writer Danny Bilson, he and writing partner Paul De Meo envisioned a James Bond story centered on a rogue MI6 operative caught between rival criminal empires led by Dr. No and Auric Goldfinger. Although they had to comply with creative restrictions imposed by EON Productions and MGM, the project moved into pre-production at EA Los Angeles, but ran into problems almost immediately.

EA wanted the game completed on a roughly nine-month schedule in order to maintain its annual James Bond release strategy, with James Bond 007: From Russia with Love already planned for the following year. EA Los Angeles manager John Batter chose the title GoldenEye: Rogue Agent for marketing purposes, despite the game having no narrative connection to either the 1995 film or the 1997 game, which Bilson felt invited unrealistic expectations and unavoidable comparisons. The project was further complicated by the studio's attempts to modernize its engine after criticism of the technology used in Medal of Honor: Rising Sun. Communication between the writers and developers gradually broke down while the engine upgrades were still unfinished, resulting in the removal of numerous storylines, scripted sequences, and large-scale gameplay moments so the game could be finished on time.

The game's production also had consequences beyond its own development. EA shifted marketing resources toward GoldenEye: Rogue Agent, reducing promotional support for the game TimeSplitters: Future Perfect. That game struggled commercially despite positive reception, whereas GoldenEye: Rogue Agent sold well despite widespread criticism. The experience ultimately convinced Bilson to leave EA, citing his growing frustration with the company's handling of the projects he had worked on, and he would not work on another video game until joining THQ in 2008.