Little solid information is revealed about the personality or propensities of System Shock's protagonist, the nameless hacker, save that he is a computer hacker of considerable skill. On April 7, 2072, as he attempts to hack TriOptimum's corporate network, he unwittingly sets in motion a chain of events which nearly culminates in the destruction of Earth. Caught red-handed in the process of accessing protected information regarding TriOptimum's orbital research platform, Citadel Station, he is immediately transported to the station by TriOptimum security, where the company's Vice President Edward Diego confronts him personally. Unbeknownst to the hacker, Diego is currently being investigated by TriOptimum for suspected impropriety, and the hacker's appearance presents him with a golden opportunity to cover the trail of his past misdeeds. Diego presents the hacker with an offer he can't refuse: hack into the station's artificial intelligence, SHODAN, and hand control of it over to Diego, and he will not only be released without punishment, but will also be gifted with a military-grade neural interface, something a hacker might find especially useful. With no other viable alternative, the hacker consents. SHODAN's ethical safeguards are disabled without incident, and shortly thereafter the hacker receives his implant as promised, followed by six months of recuperative stasis.
The game begins as the hacker awakens from his slumber to find the station in a dire state. While he slept, Citadel Station slowly descended into anarchy as SHODAN, without her former ethical limitations, began slaughtering and experimenting upon the ship's crew. Not long after he is resuscitated, he receives a message from Rebecca Lansing, an anti-terrorism consultant hired by TriOptimum to contain the Citadel Station disaster. For whatever reason, the hacker's presence in the medical bay went unnoticed by SHODAN, and now that he is awake, Lansing informs him that his neural interface is their best hope of stopping SHODAN, who now plots to assault Earth. She explains that he must ultimately make his way to the bridge level of the station, where SHODAN's main CPU resides, if they are to hope to defeat her.
Over the course of the game, the hacker overcomes many obstacles and defuses all of SHODAN's threats. He disables the station's mining laser, which SHODAN planned to fire against Earth's major cities, jettisons a grove pod which housed her lethal biological experiments, and also prevents her from downloading herself into Earth's computer network. In the end, he faces off against her in cyberspace, where she is defeated completely. In gratitude for part in preventing even greater calamity, TriOptimum offers him a legitimate position within the company, though instead the hacker chooses to continue in his illicit lifestyle despite the horrendous consequences his actions had on Citadel Station.