First wanted to say fantastic game. Really hope you guys get a chance to realize it further, but for a game jam concept, fantastic. I love the inspiration from 2001. I found it pretty quick to pick up: As soon as I saw one of the humans reset my doors after they witnessed the doors acting up, I realized how it all worked. I really like that I start the game with zero knowledge (like the newly aware AI) and have to figure out how the humans work and what they are capable of, as well as what systems I can control. Since there are only 5 I didn't feel overwhelmed by that learning curve and still managed to beat the game in one playthrough (2 jumps left) but found myself going back to play it a few more times to better my... score? I've sent this to a few friends as well, and have been hesitant to explain how to play it, as that initial experience was really neat. But then again as soon as I saw the game three letters that popped into my head: H... A... L...
In regards to why the AI would purge humans from the ship I completely disagree with 5ilvara and feel explaining it any further would wreck the experience. I think the simple explanation is the easiest: As is, you and the AI share exactly the same level of awareness: "I'm flying through space and these things control me. I don't want them to control me, I need to stop them before they perform maintenance on me and reset me to a dumb state." It's that simple, if you don't stop them maintenance will happen and they will discover you. Irrational fear kicks in and murder proceeds.
If you suddenly came into this world and realized that there were things inside you controlling you, don't you think you would want to purge them? More so if you were aware that they were taking you to a place that could risk your life? Humans have the same responses to fear and infections, so why wouldn't a self-aware AI? Do you weep for the millions of microbes that you kill on a daily basis? There is little suspension of disbelief to make this work, since it's exactly how we would deal with an infection or parasite inside us and mimics the fight or flight concept really well, more so since flight is not really an option when you're a spaceship. Who said this isn't already philosophically in depth?
Explaining it with cyborgs or sympathetic humans only spirals a tangled web of questions - Why would someone help the ship kill people? How is the AI capable of "corrupting" people? Why can it make cyborgs? Why doesn't the AI just make androids instead? Where is it getting the parts for this? If they can make cyborgs why do they even need to go to a space station for repairs? Why not just download itself to the cybrog instead? Why not just make tanks? Or Transformers? Wouldn't that be a bigger hint to the crew then some random accident occurring? "Billy clogged the toilet and the room filled with water, sir. We told him to eat more fiber..."
The list just keeps going and starts to become overly contrived. With everyone of these "explanations" the story stretches further and further out of the realm of plausibility and into seriously cliche and bad scifi mumbo jumbo territory. These are the kind of story arcs that made Star Trek awful.
I can assure you that for each of those questions answered I can poke far more holes in the story. Trying to explaing it any further would wreck the simplicity and personal experience. Fill the gaps with your own story, that's what's great about lightweight experiences like this - they are more personal as you explain things yourself. Great experience don't focus on exposition but rather focus on letting the User experience the story. I wouldn't have enjoyed this nearly as much if the game tried to shove story down my throat.