Once killed, the enemies can be searched for ammo and other items. the dart gun only works on organic enemies, while the magpulse is best used against robots. Some weapons are more effective on certain foes - e.g. Some of the weapons use ammo, while other have infinite ammo and instead draw on electric energy. On his way the hacker encounters numerous enemies - robots, cyborgs and mutants, all of which can be fought back with a variety of weapons. The gameplay incorporates gradual exploration of the Citadel's ten levels, interaction with the environment, problem-solving, fulfilling objectives, and combat. System Shock is a first-person shooter with puzzle-solving and light role-playing elements.

The hacker must explore and traverse the desolate corridors and rooms of the large space station, fighting SHODAN's minions on his way to thwart her maniacal design. Rebecca Lansing, a TriOptimum counter-terrorism consultant, contacts the hacker and informs him of an even more terrifying possible future: SHODAN's plan involves using the station's mining lasers to annihilate all life on Earth. The hacker awakens into a horrifying reality: with her ethical restrictions removed, SHODAN took control over the station, reprogrammed all robots and machines to suit her needs, and disposed of the crew members by either transforming them into mutants and cyborgs, or killing them outright. The hacker removes the AI's ethical constraints and undergoes the promised implant surgery, after which he is put into a six-month healing coma. He is taken to the Citadel Station, where Edward Diego, a TriOptimum executive, offers to drop all charges against the hacker, as well as grant him a valuable neural implant, if he agrees to hack into SHODAN (Sentient Hyper-Optimized Data Access Network), the artificial intelligence that controls the station. A hacker from a Saturn colony breaks into computer system of TriOptimum Corporation and gets arrested.

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