The player resumes control of the hacker after they wake up from their medical pod months later to find that the station is now devoid of human life, with its former inhabitants having either been killed or transformed into mutated monsters courtesy of SHODAN, who now sees herself as a god destined to eradicate humanity. The player must scavenge weapons, tools and equipment to survive the monsters and hostile androids now roaming the station while looking for a way to foil SHODAN's plans and escape. Audio logs left behind by the station's former inhabitants reveal details about the story and clues concerning the player's objectives, such as door codes to access certain areas.
If the player is killed by an enemy, they will have to reload a previous save, unless they have activated a respawn unit which will reconstruct their body and allow them to continue from there. Certain areas also contain terminals which allow the player to enter cyberspace, a 3D environment in which the player controls a virtual avatar with the ability to disable security measures around the station by shooting nodes. However, cyberspace contains enemies which will attempt to impede the player's progress by returning fire. SHODAN's current hold over a floor of the station is represented by a security level, which can be lowered by destroying cameras and other security systems. The security level must drop below a certain percentage before some areas can be accessed.
