@Jester: there is a walkthrough in the readme if you get stuck. And no, you don't have to kill the nautilus prime (as it's called) - in fact it's an optional boss, but totally worth it. Hey, if you do beat it without the energy form (i.e. by throwing rocks at it...) it would be quite an achievement.
Also the mainsite is back up and has been for a while.
Kinda off-topic: I also reccomend checking out
TIGSource (the indie gaming source, which is run by the artist of aquaria and has a lot of links/reviews of cool indie games as well as a large community.