Man these consecutive boss battles at the end of Cave Story are hard.
I aboslutely adored Cave Story and regret not playing it before I did. It was a very charming, atmospheric, and well-made platformer that is very deserving of some sort of sequel.
Also, aren't you referring to, IIRC, the doctor, misery, and the undead core? I remember finding the earlier ending and feeling disappointed at the fact that I couldnt save the island, but then I read a walkthrough and continued to play through the rest of the content. I should really play it again whenever I find the spare time.