So I'll elaborate on my problems with the story. These problems of which aren't entirely your fault, but a lot of it falls into the category of "Fanboy weeabo who thinks he knows best". I'm reciting these problems from memory, mind you; but if the problem itself is more memorable than what might have been an already-existing solution, then it's still just as equally a problem.
1) Who the fuck is "Asura"?
I had to seriously open the game in Booster's Lab to double check the name, it was so generic and unmemorable. But I did remember that this character was not only completely unexplained prior to the mirror fragments, but he seemed to suddenly become the final boss for no reason whatsoever. This was not a character created by or inspired by the original mod's unfinished state - you made this thing up completely on your own merit, and it simply doesn't fit.
"Ballos" in the original Cave Story may not have been properly introduced until the extra dungeon, but he has a hell of a lot more backstory than "Asura", and a much more original name to boot. The first time we're informed of Ballos' existence is in an ominous bonus scene as you set up your game for the extra dungeon, followed by additional information to give you an understanding of who Ballos is, and what he had become.
But "Asura"? All we're told is he was some demon sealed away in a shitty mirror that you phoned into the game for seemingly no reason. I was under the impression that this mirror was going to be a usable item that would teleport you to a hellish bonus dungeon on the spot outside the plot -- a much, MUCH better idea than was executed -- and instead you turned this phoned in apparition into the only final boss of the game.
Ballos EXCITED me, and STILL does with his imposing backstory greeting you every run through Sacred Ground. But "Asura"? I don't know who he is.
2) Who the fuck is this other "Genesis"?
I see what you did here. I have the game open in Booster's Lab, and I can see three things.
i) There is no "Defeated Genesis!" after the Genesis: Source boss.
ii) Misery's easily missable and entirely not worth it in the slightest extra text taunting you sloppily with what you think is "foreboding" but is actually "bad writing"
iii) You're an idiot.
Besides this, it's my understanding that even if you beat the "real" Genesis (Who is incredibly phoned in and disruptively sloppy), you die and game over unless you have some stupid mirror you added just because you like shiny things. This not only ruins the game itself as an overarching story, but this tell me that you really, REALLY think that "Don't tell the player anything until the big reveal!" is a good way to write a story. Please see (iii) for my, and anyone who's older than 20's, response to that idea.
3) What the fuck is going on with King?
We get it! King was your all time favorite Mimiga character! His death was tragic! You didn't like him dying! You wanted to write fanfiction! "But he's dead! HOW DO I DO THAT?"
Luckily, you completely misunderstand referential sequencing in art. What was originally a reference specifically, and ONLY to point out that the blade was still on the island and still housed King's soul, you turned into a destructively bad idea that King was "still alive" in some way or form, so you could plaster him all over the walls for your own lazy story telling. In fact, you went so far to do this that you decided King's sword should be even more magic and better than the original! So you made it BLOOD CRIMSON RED AND PUT THE WORD "TIME" IN ITS NAME! HOLY FUCK, WATCH OUT STEPHEN KING WE GOT A FUCKIN' SHAKESPHERE UP IN THIS CRIB!
4) What the fuck is even the hell?
As I said a few posts ago, the original Jenka's Nightmare wasn't a masterpiece of sequential storytelling, nor was it even very passable in the first place. I was personally entirely confused after Genesis: Water because I didn't know what was going on. I wasn't told to go here by the game, and nothing in the game coincides with even being there. Which generally means it's filler.
This could be fixed mind you, and a better explanation could be given for each individual area. This is the point of the 'Cthulhu' NPCs - mysterious bystanders who hand out third-person information onto the area and story without shoving it down your throat. In fact, from memory, I don't recall seeing one ever again after the Labyrinth circle maze, and it would do well to have them breath a bit of life into the areas that are otherwise boring and meaningless to the plot.
5) Why the fuck do all the characters from your half of the game refer to Quote as 'soldier'?
No seriously, what the fuck? This isn't foreboding anything or referring to anything. It's just dumb.