Well, I just have one final say one this.
Upon defeating the Core, a massive earthquake was sent through the island, as a result of a sudden imbalance. The Core, which holds some sort of control over water (hence the rise and fall of water during the battle) acted as the balance. Once that was removed, like popping a balloon, all the water it surpressed before had suddenly had an opening, leaving a certain facility in ruins and flooding a certain part of the island. (the room the core was in as well as the previous room, and the waterways, the highspeed area where you fought Ironhead was the water being released due to the fact that there was nothing holding it back anymore (which the Core was doing, until Quote nearly killed it [it was incapacitated and nearly dead as a result]))
Also, @Kirbyarm
I understand the concept of too short a game, however, it was fairly evident at that point that there was more beyond that. Plus, we are talking about current Cave Story, not any of it's previous betas or otherwise.
Irregardless, I don't quite get what you are getting at. Sorry, but it seems you are refferring to the Bad ending. While it does indeed come after the ruined egg corridor, I am none too sure as to why you choose to talk about that.
Also, ya really didn't offer up that much of an explanation for a cause to the explosion. Sorry, don't mean to really bash ya for that, just pointing it out.
Also, out of curiousity, you called yourself an "experienced game designer". May I ask of what? Don't mean to derail the thread, I'm just rather curious about the last bit.
Oh, and welcome to the forums.