The original translation by Aeon Genesis wasn't used because of an inability on Nicalis's part to get licensing done to use it, so they went with their own and tossed the old one out, which gave us such lines like Balrog's ' OH YEAAAH!' and other gems. They take the indie-favorite Cave Story, slap on some shiny new graphics and music, and re-translate the story from the ground up.
Cave Story + (and its brethren, Cave Story Wii and the OS X port) are games released by Nicalis over the last few months.