massive spoilers - please do not read if you haven't completed Aquaria!
I got the full end sequence by finding all of Naija's lost memories. I don't understand the ending though. I got the main point of it all, boys falls in water after his world dies, spirit resurrects boy as a god, god creates mother, mother creates Naija, god goes mental, Naija kills god, the end. So what's with the man and the flying boat thing? Is that a grown up Naija on the bed? And then there's the Aquarian text right at the very end (just after "To Be Continued")....although I think it reads The End, not that I can read Aquarian language it's just logical that it says The End.