Reading this AU and especially these more "serious" installments of it, it really feels like you're getting into the heart of what the Cult route was trying to message but (IMO) was a bit clouded/hindered by having to adhere to/address the sci-fi/war premise and setting of the main storyline. Having them in a more casual setting like this makes it a bit easier to recognize and really sympathize with the tragedy of them being predetermined to be prevented in turn from reaching mutual understanding, because of some post-traumatic reaction from beyond their control...
I was so touched by the Le Petit Prince paraphrasal... the headcanon of that (or its apprpriate in-universe equivalent) being Aotsuki's favorite book is SO painfully ironic and therefore SO good... I love the idea of him being internally such a bleeding heart romantic and yet due to The Circumstances being unable to form any meaningful connections himself... and that turning him obsessive and just further ruining his prospects... and despite all this he would stubbornly never admit to having been sucked into that sort of self-fulfilling prophecy. (Sorry for the tangent. Please interpret it to mean that you handled the character writing succinctly)
There being audio in the game was a nice surprise, and the msuic choices contributed well to the feel of the scenes, so I wanted to shout that out as well in this comment.
The ending OUGH... as a proponent of #torturetakumi I must admit that I love to see him warping himself for the sake of a normatively well-intentioned goal, and finally reaching it only to find that he can no longer enjoy it. That was my main takeaway of his character arc(s) in the truth routes of the game, and you similarly nailed it here. [wearing 3D glasses and with a bag of popcorn in hand] Somebody put that red thing through the wringer some more!
Seriously though, thank you for creating and sharing this!