One thing about Gaius bugs me. He is very close to the Queen and the first heir Luci. Given how much they trust him, there is a very good chance he is aware about the fleshbot army.
But given how pretty much he is under their thumb, I've this sneaky suspicion he has convinced himself, that the bots's existence is for the greater good. Like how this will save so many other lives and that science is a force for good in the right hands, no matter what the method employed. Especially given his husband is alive because of these advances.
This is also the reason I made one choice amendment at the end of the second last update. When I saw the bot army, I reloaded an old save from the ship when I was talking with Gaius, and amended my answer to his question about "What do you think of New Antioch". Initially, I supported it as a good thing, but after seeing the end, I changed the answer to a more neutral "I'm not sure what I think about it." You actually loose favor with Gaius if you don't think positively about the city, which makes me think that either he has been kept in the dark about the bots or he knows about them and still thinks the city is in the right.
Whatever the truth, one of two things might happen. Gaius will either be made aware of the truth and will suffer a crisis of faith and duty pretty much becoming emotionally paralyzed. Orrrrr he will challenge MC to take a side and will stand in his way to defend the royalty, which will inevitably end up with MC killing a good friend.