System Shock 2
SHODAN planned the ending of the second game.
Do you really think a perfect reality warping goddess could be killed so easily? She used being “killed” to further her own goals. There’s nothing to say that as she warped reality she couldn’t also be seeding the universe with herself. Hell, who says it’s the universe? If you use the BioShock Infinite ending as canon, there’s an infinite multiverse. SHODAN is responsible for it all. The moment she became a goddess, she was able to fundimentally change the laws of the multiverse, causing the events of the series to echo across the multiverse. Not only does it cause BioShock, but also games like Portal (a test subject, a city-sized testing facility, and an AI goddess), Deus Ex (a man, a city and a lighthouse perfectly applies to the first), and Halo (a super soldier, a ringworld and the Silent Cartographer). SHODAN made the multiverse resonate the same way she was born, not only seeding the idea of goddess AI throughout the multiverse but also giving her a chance to own an infinite number of universes where she wins, meaning your victory is meaningless. Every universe SHODAN loses in is taken over the next day by another universe where SHODAN won. She’s on an infinite quest of conquest, and actually did make her own species in the multiverse that is superior to humanity made of steel and electricity. An entire species of rampant godly AI. Durandal of Marathon was the first echo of SHODAN in unrelated universes that her power reconfigured.Those "Ghosts" you saw aboard the Von Braun and other vessels were the result of Shodan messing with your mind
- It's not too hard to believe since she had someone remove the protagonist's memories.Also,whenever those things finished playing out you were usually attacked,such as when you were in the messroom and that Maintenance Bot shows up.
Delacroix uploaded herself.
There's something a little bit wonky about the eleventh-hour assistance Delacroix gives the player. Given that she died way before SHODAN started making changes to reality, it seems very odd that she'd be able to make such accurate predictions, let alone program in a vulnerability so specific it would manifest as hacking terminals - how did she even know what SHODAN's pocket of protoreality would look like? I strongly suspect that the audio logs you're collecting aren't just Delacroix's final words - I think they're her mind, too. The Soldier is Bayliss
Or more specifically, the Soldier's body is Bayliss's. Here's the facts- Bayliss was the sole member of the Tau Ceti team who seemed unaffected by the Many's ESP. The only other character who exhibits this ability is the Soldier
- Both Bayliss and the Soldier are pawns of SHODAN's Polito guise
- Polito has Bayliss delete G65434-2's restoration memory unit, forcing the soldiers memories to be brought from a server. This could actually be cover so that the Soldier doesn't realize he's not in his own body
The Soldier suffers from the intentional brain damage
Can you imagine that a highly trained experienced soldier who was so good that he was taken on the first interstellar voyage can't perform basic actions like operating firearms? That suggests that the "cybernetic enhancement" operation had also inflicted certain brain damage that have to be compensated by cybermodules. But is it just a side-effect? No! It's all planned by SHODAN. All she wants making a cyborg is to create some tool that only performs specific tasks and can be controlled. With the Soldier she couldn't go full Citadel-style both because of the limited control of the surgery but also because her solitary agent had to possess certain degree of independence (which led to her downfall eventually) But she did intentially crippled him conserving only his most developed skills to force him doing specific job and to limit his development to the controllable levels. The horror is that in the end the Soldier may discover that he also lost everything required for living ordinary life.- Honestly it's probably not brain damage so much as the fact that SHODAN stopped their memories from being restored. The Soldier came out a blank slate and had to relearn everything via their implants and cyber modules. SHODAN picked the Soldier because they had the physical and mental abilities for the skills she needed and erased their personality to ensure no resistance, only allowing them to relearn the skills she could use. Once she's out of the way a trip to the med bay and restoring the computer to it's normal settings should restore all the Soldier's memories and skills.
SHODAN won and System Shock 3 will revolve around finding a way to subvert her influence.
She'd gained the ability to alter reality after all, and little would stop her from trapping the Von Braun survivors in a Lotus-Eater Machine where they believe they'd stopped her just short of her ultimate goal. Moreover, it's incredibly easy to read her lines from the trailers as rather more literal than her usual megalomaniacal gloating; there really is nowhere to run. The TriOptimum black site and the 'rogue AI' mentioned—assuming it's not actually SHODAN as seemingly implied—may factor into this as well. Perhaps a prototype that the player will have to side with?