Black Omen from Chrono Trigger:
What it looks like:
What it really is:
Because the top of the structure is really this part:
The Black Omen is a Star Destroyer and not some sort of weird-ass flying tower.
The last image still doesn't make sense to me though, particularly the zoom-in. If the Black Omen is a star destroyer, shouldn't you be able to see the lower/main level of the ship in the background as opposed to the moon over the horizon?