Read through the whole thing in one sitting. The core plot it presents is interesting, but at times I do feel like the phrasing and some scenes' pacing could be done better. It would be good to get a proper writer/editor to look through it and suggest some changes, but it's not so bad that it ruins the story, maybe at the level of feeling like a slightly awkward translation. Otherwise, the presentation is very good, way above what I would normally expect from most VNs.
Considering the impact that Anastasia's release is supposed to have, her sudden disappearance only to show up again in the next section so abruptly out of nowhere is weird. I get that it's hinting that something weird is going on with her, especially with the Theseus discussion afterwards, but I feel like you could've let the matter rest and breathe for a while more before bringing her back out of nowhere so quickly. Maybe explain more on the plans they've been saving up all their money for and how it's continued since the explosion.
The references to philosophy concepts does feel a bit on the nose. You really needed to do a Ship of Theseus argument on the ship owned by a guy actually just called Theseus, who himself keeps replacing and repairing stuff on said ship? This conversation feels like it'll have more important meaning later on, so sure, but calling the guy Theseus too is a bit much. Similarly, the Monty Hall problem reference just feels very out of place. I'm not sure what swearing off probabilities is supposed to signal for future plot details, as compared to the conversation on Theseus. When they were talking about the genetic modification project, I just knew it was going to be called Prometheus as soon as they mentioned stealing from the silicons.
It gets to a point where it just seems annoying, because the kind of people who read these kinds of things are probably well-read enough to know a lot of these kinds of concepts, and it's somewhat insulting to be repeating the whole thing back to them and specifically drawing attention to it. If IRYS is an intelligent AI, it shouldn't be questioning why Alcides chooses to switch, because it too, should also know that the probability of picking the right door is higher if he changes doors. This also seems to be the only time I can remember it asking or questioning the user about a decision, which is why it's so strange to me. And really, it could just be a binary decision where he picks wrongly, gets hit, and then takes the right door after recovering.
I also feel like it takes too long to get to the primary goal of the Aenigmas and their place in carbon society. They're sneaking around to build something of their own, but they still appear to live within carbon society, somehow able to earn money while also apparently having bounties on them? They're said to be used by carbons, but I still have no idea what they're actually used for if they've still got all the time to salvage parts for their new base. They're part of Prometheus, sure, but it doesn't look like they're really making any science stuff aside from maybe Anastasia knowing all kinds of things.
Some of the tech stuff doesn't really make sense to me. How did the Nexus experiment kill Trafalgar again? It has something to do with him connecting to the power supply, but I don't recall any mention of him connecting to the Nexus itself if they're just in their ships in some ruins somewhere else.