Excellent atmosphere and fantastic story telling!! The story may be simple, but it's engaging, I love the whole presentation a lot!!
Quite an issue is actually the readability of this game. The colour scheme makes it hard to spot the bullets on the screen. It doesn't impact the difficulty of the game (as there hardly is any), but it's still unpleasant. It also makes the turrets on the big ship almost invisible. A few simple outlines might already solve this problem (I know these outlines may effect the visuals a bit, but it makes the game more comfortable to play).
Also, the mouse controls don't make any sense as the only thing on the mouse available is the left mouse button. You could remove that entirely and make the main menu controllable via keyboard, that would be great. (The main menu font is pretty unreadable to, I have no idea what settings were available in that sub-menu).
Still, an awesome game I enjoyed a lot! Great job!