Well, this story is NEVER gonna be finished (at least, not by me), so here's what I was planning to do with it.
First things first, let's discuss the backstory. I was going to reveal this very late in the story, just before (or maybe even after) the climax.
The Candypop Buds were created by the Plasm Wraith, who was created by some scientist who lives in Johnny's hometown. The Plasm Wraith hates this scientist, so it decided to study human behavior so it could take control of a human's body and kill the scientist. For some reason, it thought the best way to study human behavior was to kidnap seven humans and put them in Pikmin bodies.
Now that we have the backstory done with, here's what would have happened in the rest of the story:
-The Winged Onion is found easily
-The White Onion can't be found before sundown, so Rosa has to stay on the surface. Dave stays with her to help keep her from getting killed
-The White Onion is eventually found
-Three more characters are introduced: Lee Urbina, a Latino weeaboo, Ashe Urbina, Lee's transgender twin, and Douglas Irving, a detective.
-A cave is discovered (from here on out called "Intruders' Tomb")
-Johnny and co. head down Intruders' Tomb, they all come close to death
-They leave the Intruders' Tomb to recover
-They come back later and they're prepared this time
-They head to the bottom of the Intruders' Tomb
-Epic fight with the Plasm Wraith
-Plasm Wraith gets beaten
-Because the Wraith is defeated, Johnny and co. become human again
-And then Johnny becomes the protagonist of a JoJo's Bizarre Adventure fancomic
Yeah, I was planning to take the main character of this Pikmin fanfic and make him the main character of a JoJo fanfic. He was going to have a really overpowered Stand.
If you think that's weird, you don't even wanna KNOW what sort of crazy backstory I threw together for Pikmin Colors… (There's a reason why the name of Johnny's mom was Alex. It's a Minecraft reference. Yes, she was supposed to be Alex from Minecraft. No, I don't understand why I thought this was remotely reasonable as a backstory for a Pikmin fanfic.)
Oh, also, I never mentioned it in the story, but Rosa was black. (I was originally going to mention it in chapter 4, but I decided not to.)