Some really great layout and design choices here. I love the flow-chart map. The texturing and art is great; where did the faceless portraits come from? I really like them.
I may have been tempted to swap the NPC information with the 'Matron Destroyed' and 'Random Encounters' type blocks, but that's likely a matter of personal taste. My only other feedback is that I wish the Ancient-Myth of it all was a little more front and centre. All in all, this is a solid entry, strong on Mothership vibes and with great presentation.