It's basically left up to our imagination but, I've trying to keep in mind any clues left by Pixel; for instance why doesn't the landing expedition in Cave Story find the crown almost immediately; being out in the open next to ruins; and sitting on a throne
Whether this is intentional, the opening scene is dark inside that throne room, so I imagine the throne room was buried~ And there must be another way to get there
And there must be plenty of ruins on the island for the scientists to not really immediately go for the prize...
Maybe a city with a similar story to Pompeii? [Except Ballos...and the castle~!]
http://upload.wikimedia.org/wikipedia/commons/5/5c/Pompeii_the_last_day_1.jpg
yeah that must be it... as seen in "hell" the city/castle must have been buried for the most part~
er that's what I'm thinking anyways
oh and f-ram.net! You did a good job as well~! Seeing various perspectives may lead to some truth...