I like the stealth style of this game. Having to avoid all the plague doctors along side trying to cure the shadow meter allows for the player to focus on multiple threats rather than simply just running away. Under you Extra Notes sections you mention a few mechanics that may not be recognised. I did not notice them in the game, but if they were to be more balanced and effective I think they will add a lot more to the difficulty of the game, and add more threats for the user to try and control.
I didn't really understand the elixir system at first, but I understand what the goal of them are meant to be.
One critique I have is that the game in terms of movement felt a bit directionless, as in at first I wasn't really sure if I am meant to heading in a certain direction or just wonder around to find materials.
Overall, great work! I really enjoyed the art style and UI elements, they are really consistent with each other and suit the theme perfectly. Awesome job!