Aha, make it night once you get on the Moon platform in Ryoshima Coast, it's near the beginning. There will be a space with a huge structure at the end. (Not that hard to see, you have to have Double-Jump to make it.) And then you lillypad to the ship, and go into the portal.
I loved the ship. Killing the green hands once you drain the place is my favorite part. 8D Even though it's not necessary, I do it for fun, and to get Praise.