Pill_Guy
I'll be honest, Willard moves out of his safe zone too frequently. He isn't acting the paranoid, deranged genius that you set him up as. I'm hoping that the new psionics can take him down a peg in terms of hypnosis/brainwashing. Allowing the MC to partner with the AI for the forseeable future is also a fantastic move. If MC can manage to ingratiate himself to Shepard before rank 3's planned take over, that'd be tight.
The thing I love about this novel is the depth of events that we don't directly see. It's easy to give the appearance that more is going on without doing much work (like the grade two sausages) but far harder to constructed a series of events that isn't obvious, while giving the reader enough information to figure it out. Only with this chapter do I finally feel like I fully understand the chain of events from Cindy disappearing to killing Sheila and finally to her partner's death. And it all makes perfect sense now that we know how the AI behaves, even though you haven't directly explained much of the events themselves.
So if the AI prioritizes the higher-up individuals wouldn't the MC have been part of that higher-up? His project was extremely important for the future survival of those people by extending their meat food supplies and potentially improving their fertility rates. Yet he's been put into conflict with Shepard since the start. If that's the reasoning behind the whole confrontation it just doesn't make sense.