System Shock 2, according to its pitch document, was originally titled "Junction Point". It was intended to expand upon the role-playing element of the original System Shock, which itself was intended to bring the gameplay of another of their games, Ultima Underworld: The Stygian Abyss, into a science fiction setting.

The first System Shock was generally perceived to be a Doom clone, and the developers blamed this for its limited commercial success. With Junction Point, their goal was to add significant role-playing elements and a persistent storyline so as to distance the game from Doom.