I think the UI disappearing is a bug that may be caused by playing the browser version (the game is large enough that sometimes not everything loads, when the game tries to draw an unloaded file everything downstream breaks too) if you are already playing the downloadable version, then that's a major bug I don't know the cause of.
In general to play the game the first thing to master is using the 'z' key and hovering over things you don't know what they do. The way to shoot is to put people in the weapons room, and shields is the shield room. That's the basics. There's also a tutorial but it's more or less what I just said extended.