I love this so, so much. I actually guessed the truth quite early on and was pretty sure where the plot was going - but that didn't stop me from melting and almost tearing up when the resolution actually came. That, my dear author, is one of the highest compliments I can think of. Just. The FEELINGS.
Some other comments have mentioned how "stereotypical" Phebe is as an otome protagonist. I agree wholeheartedly. This story is ultimately about Phebe and her growth, not the boys, and that is one of the most brilliant twists in this genre.
Your writing is absolutely gorgeous. There's a touch of gentleness to it that enhances both the sadness and the bittersweetness of the story. The relatively minimalist visuals also serve the atmosphere of the game perfectly.
Really well done. My utmost respect to you and this game.