This was such a thick story. It took me a while to realize there were humans, if they could still be called that. The girlfriend was so cold in her reality, like a machine, eating her food without joy, only her function mattering to her, to work up through the government. The same for the antagonist who manipulated the farming creatures for her own ends.
Yet the machines, through intervention, were moving in a different direction, towards insight and knowledge. I don't really understand how the unknown woman could know the machines would react this way. It implies a greater amount of knowledge of the machines beyond normal insight. She may know how this station works at a higher level, but it seems so sad she would use that knowledge in such a shallow, selfish way, no greater insight gained.
Hector seems to think little of himself, worshiping a woman who only sees him as a failed project. She didn't understand that Hector did not need any fixing, as he was learning to enjoy his life, savoring the food and drink, enjoying what his life had to offer. He has learned to respect the farmer creatures and learned from them where others see them as mere devices. In his respect, he may have built a blind spot, not realizing sooner what could be happening. Of course, had a terrorist attack not occurred in a long time, no reason for him to understand the source of the dream. If anything, it exacerbated his own faith confusion, forcing him to face his own doubts and beliefs, which were so bashed by his girlfriend. It really is important to have relationships with people who build you up and see your positive attributes, not people who only focus on your weaknesses in order to "fix" you.
It was a deep story worth a second listen.