I absolutely love everything. The gameplay, the story, the graphics, the audio... everything. I have no constructive/negative feedback to give you, only praise. Very well done, I love it.
There is only a single issue. You don't lock the mouse to the screen and you don't allow fullscreen mode. I would allow the player to play in fullscreen, in one of the levels I kept pressing outside of the game and dying because of it. There's an option in Godot to scale the window properly, it's on Display->Window->Stretch. And then you need to play with the options.
But overall, a very solid game! Good job!