Warning, spoilers for the ending of System Shock.
In the original System Shock, the ending sees the Hacker (you, the player character) enter Cyberspace and take down SHODAN, AKA the Sentient Hyper-Optimized Data Access Network. Victorious, you return to Earth and are heralded as the hero of Tri0ptimum, but System Shock nearly took a different turn for its finale.
Speaking to RockPaperShotgun about the history of System Shock, programmer Rob Fermier revealed, "The original ending of the game was gonna be that when you defeated SHODAN, we would make it look like you had crashed to desktop. Your commands wouldn't work, and you would start to think that SHODAN had come into your actual PC."
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Something about retro games is creepy enough, but I can't imagine finishing a six-hour session of System Shock at night ending with my desktop and SHODAN breaching my files and infiltrating my system. It sounds terrifying, especially in the early days of the internet where this would've become playground chatter that your mates wouldn't believe. 'Sure James, I bet the villain hacked your PC'. It sounds like a Herobrine joke.
On a more meta level, SHODAN was designed to represent the developers, a sentient AI that viewed the player as an enemy, someone who would spend their time in the game trying to break boundaries or sneak past objectives. Essentially, SHODAN was Looking Glass Studios trying to catch speedrunners in the middle of glitches.
"In a sense, SHODAN would represent us," designer Austin Grossman said. "We would have all these triggers in the world, and we would be seeing through the triggers what the player was doing, and we'd be commenting on it. It turned
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