So basically it will be at an indeterminate time period after the war. Many droids are still alive and kicking at this point, possibly repaired or recreated. The island is full of new mimigas and has small bustling towns but no real center. The island is much bigger with new areas to explore.

I need to know if anyone is interested and what level of post quality should I make this?

Interested, just curious about the execution. Given Cave Story's relative rarity nowadays (in my experience), an overall story refresher for everyone might not be out of line. I'm a bit curious about the execution, but I also trust that you'll have ways to keep the plot starting and moving forward. As for level of posting, I'd say Casual would be good for this, given the possible characters presented here.

Speaking of, who will we play as? I assume either Mimigas or Surface-Robots, but maybe you have something different in mind.

Humans rarely, surface robots rarely, and mimigas commonly.

The execution will involve going about and solving puzzles to get pieces of a war machine to stop the next doctor when he comes. Also it will be a townish experience until the new doctor comes and the machine needs activating.