I see, so it's more like "Nomura had this story in his head", like with KH II originally after KH 1 but was not sure if he would have the opportunity to show it somehow as the only one definitely planned to be "provided" was Birth by Sleep.
Did you even read the interviews Grass posted? Nomura did not have a story in his head. He had to make one up from scratch at Nintendo's request. If you follow all the interviews, including Kanemaki's, the process for Days was more like:
Nintendo: Hey Nomura man your KH series is pretty popular. We're going to release this thing called the DS, do you want to make a title for it? That would boost early sales.
Nomura: Sure thing bros. I don't have any ideas though... WAIT I just got this really awesome idea. Can I make a DS game called The World Ends With You instead?
Nintendo: Sure whatevs, just make us a KH game at some point.
Nomura: *makes TWEWY* Hmm. Now what to do for that KH game. *looks at ideas scrapped from TWEWY* Maybe a multiplayer? With the characters fighting?
Disney: NO. Bad image, dude.
Nomura: Rats. Uhhh but I really love this idea. OH I KNOW *makes Dissidia*
Nintendo: Dude where is our KH DS game
Nomura: *working on over ten KH/FF/Parasite Eve projects in this period* What? Oh yeah. Where are my notes on that. Multiplayer. Not Disney characters though. OH OH I COULD USE THE ORGANISATION! That will be so cool, they can fight and shit, I even made them with all different styles and elements. I am so smart. What should I do for the plot though. *looks at pile of other projects* I don't have time for this shit. Ummm Watanabe?
Watanabe: I am working on BBS AND Coded man, I got enough on my plate. I'll supervise but I'm not writing your goddamn scenario again
Nomura: Crap. Um... Nojima?
Nojima: Dood I don't even work for square any more
Nomura: POOP. What do I do. Why do I make my plots so freaking complicated, means there are only a handful of people on the planet who could write a... *sees the game novels on his shelf* EUREKA! Kanemaki?
Kanemaki: OMG NOMURA OF COURSE I WILL WORK FOR YOU I WILL ALSO HAVE YOUR BABIES
Nomura: I am pretty amazing *polishes belts* Do you have any experience with video game scenarios?
Kanemaki: WELL I DID ONE GAME AND IT WAS DEFINITELY NOT A YAOI PORN DATING SIM NOPE
Nomura: ...Maybe I should get Ishida to help you. Anyway you're hired!
Kanemaki: ON ONE CONDITION THOUGH I AM YOUR BIGGEST FAN CAN YOU DRAW ME A NEW FEMALE CHARACTER WITH HAIR LIKE MINE
Nomura: *looks at his pile of projects, looks at clock* ....Sure. That won't take long, I guess.
Kanemaki: OH THANK YOU SIR YOU WILL NOT REGRET THIS
Nomura: (laughs)
months later
Kanemaki: HERE IS YOUR SCENARIO I WORKED REALLY HARD ON IT
Nomura: Oh fuck... okay, give me two weeks and I'll turn this into a script.... somehow...