Upon the closing of Plasma's Folly, I promised to reveal all of the plot twists I currently have in my head. I'll also provide an explanation as to where they fit in with the plot, and why I chose to use them.

# 1 - Ghetsis is a Genesect Hybrid
This was probably the easiest twist to guess, and I wouldn't be surprised if some of you figured it out beforehand. It was frequently hinted at, the most obvious example of Ghetsis's desire to become a hybrid being found here:
Ghetsis silently crept up behind the scientist, who was slowly typing something, his hands shaking. "Excuse me," Ghetsis began, trying to sound as politely as possible.
The scientist jumped, and cried out in alarm. He then whipped around in his chair, and pulled his head back at the sight of Ghetsis. "W-what?"
"You know how that traitor created that formula, don't you?" Ghetsis questioned, a grin spreading across his face.
"Yeah?" the scientist replied almost shyly.
"So, with that knowledge, you could recreate the formula, correct?" Ghetsis was beaming.
"Possibly? Why?" the scientist looked slightly frightened.
"Haha," Ghetsis snickered, his voice growing louder, "bwahahahaha!" His laughter rang through the air, causing the scientist to wince.
"I don't like the sound of this," the scientist muttered under his breath.
Additionally, all (I think) of our encounters with Genesect following the original escaping the lab were actually Ghetsis in Pokemon form. That's why "Genesect" had a completely different temperament and behaved differently from the one in the lab. I also recall at one point I described a creature watching the hybrids from the bushes when they were heading to Mistralton; again, this was Ghetsis, and this is why he knew to go to Nimbasa.
Ghetsis intentions are more thoroughly described further down.

# 2 - N is a Zorua/Zoroark
You're probably thinking something along the lines of, Hmm, where have I heard this before... Yes, I do realize a twist very similar to this appeared at the end of the original PMD roleplay, and it bothered me to be considering this twist at first. At Rainy's approval I decided to go with it anyway. It really did make sense, in my mind at least; it worked much more nicely than how it turned out in PMD. So, I guess we could say the PMD thing was a prototype for this. I've had this idea in my head since the beginning of the roleplay, and I always passed it off as some stupid thing until I was inspired by the list of facts about N that was revealed a while ago, with this tidbit in particular:
"N believes he was born from Pokemon; the parents are unknown."
N isn't Ghetsis's son. He's not even human. Rather, he's a Zorua Ghetsis obtained as an egg and raised from birth. Zorua has been shown to be a highly intelligent Pokemon; for example, the one in that stupid movie could speak with telepathy and whatever. Ghetsis raised the critter, and brainwashed it into becoming this N character. He modeled the human persona N assumes after himself to create the illusion that he was his child. No one knows about N's true identity as a Zorua, except for the Shadow Triad, Ghetsis's most loyal followers. Ghetsis chose to raise a Pokemon rather than a real child to accomplish his goals because Pokemon are far more obedient than humans. Zorua's high intelligence, as well as its ability to shapeshift, made it the ideal Pokemon to use. Also, Ghetsis couldn't abduct a real child because then he'd be arrested and he wouldn't want that. But what set N apart from a real child was simply that he wasn't human. No matter what Ghetsis brainwashed him to believe, N could never be human. That's part of why he's so socially inept, and why he has such strong connections with Pokemon. He has difficulty comprehending human morals and ambition, because he relies on only instinct and the morals Ghetsis shoved down his throat. Despite this, N questions whether he truly identifies as a Pokemon or a human, because he's spent almost all his life as this N persona to the point that it's basically become his natural form. Or perhaps he's so used to being N that he's forgotten his true identity. Anyway, the hybrids and GMP649 and such obviously go against what N was raised to believe. They were supposed to be kept hidden, but obviously that didn't work out. N doesn't know how to handle these situations, because even though these modified creatures defy what he was forced to believe, at the same time they're still humans/Pokemon so it seems wrong to completely be against them. This struggle is especially present when he fuses himself with Reshiram in a last resort effort to accomplish his goals. I intend for this to tie in with the story's theme of "What separates humans from Pokemon?" and I'll be sure to go more in depth in the fic.

# 3 - GMP649 Was a Failed Attempt at Creating a Hybrid
(I'm just copying and pasting the entire email without editing it because I'm lazy.)
"Over 300 million years ago, it was feared as the strongest of hunters. It has been modified by Team Plasma. This ancient bug Pokémon was altered by Team Plasma. They upgraded the cannon on its back."
All of this? Propaganda. A creature like this never existed in the past. It's all a lie fabricated by the higher-ups in Team Plasma. They don't want the public to find out the truth about GMP649's origins. Yes, the GMP649 project is top secret, but Ghetsis eventually intended to unleash the creation upon the citizens of Unova. 
So what was he trying so desperately to hide?
GMP649 was a failed attempt at creating a hybrid by the Plasma scientists. They received a copy of the formula from the man behind the hybrid project, but there was a bit of a bug. The solution created using it was slightly off in result. When the victim (perhaps another kidnapped teen, or a grunt who may or may not have volunteered to test it) was injected, their body immediately started hideously transmogrifying. Unlike the hybrids when they morph, the victim's transformation sequence was full of excruciating pain; their skin was ripped and torn, their bones snapped and twisted, so on and so forth... and when the terrifying sequence was finally over, the scientists were left with a horribly mutant creature; a fusion of man and insect. It was like nothing they'd ever seen before; it was impossible even to identify what Pokemon the victim was supposed to be fused with.
Of course, Ghetsis was disappointed that they couldn't recreate the solution. He had most of his scientists try to find out what was wrong with the first formula and fix it, but the scientist in charge of the original project didn't exactly want to give up hope on the failed result of the first solution. Rather that simply disposing of the failure, he worked day and night to modify the mutant creature. He actually saw the mutant as a success in its own way; they had created a creature that mostly retained human intelligence and behavior, yet had the capabilities and functions (and speech) of a Pokemon. After a series of painful experiments, he successfully gave the creature an exoskeleton made of a metal-like substance, and later installed a cannon on its back. It was only then that he showed Ghetsis what he had done. Ghetsis was fascinated with the creature, but at the same time he wasn't happy with its human behavior. This goes back to how he used a Zorua to help with the spread of his ideals; humans had ideas and ambitions of their own, and weren't obedient on the same level Pokemon were. However, he conspired that this now powerful creature was perfect material to fuse someone with; since Genesect had the mentality of a human, hybrids fused with Genesect would not be unstable and wouldn't fall victim to primal rampages like people fused with real Pokemon. That's why he fused himself with Genesect once his scientists figured out the solution, and this also explains why Destiny doesn't experience primal rampages.
... And that's when I finally realized that none of this makes sense in context. There is no possible way Destiny could be a Genesect hybrid if Genesect was created by Team Plasma after the traitor scientist was apprehended. I don't know how I didn't notice that earlier. Actually, I originally had it so it would work out, but I kind of went out on a whim and altered it so it contradicted the storyline without realizing it. So now I'm going to attempt to change it so it still works.
I would've said that Destiny was an experimental Genesect hybrid created by Team Plasma that was completely separate from the traitor scientist's creations, but that just wouldn't work out with the flow of the story. Actually, if you really think about it, none of what I had would work. So instead, maybe I'll actually draw inspiration from my plans for the roleplay for this.
It was Ghetsis's original idea to create Pokemon hybrids. He would use them to enforce his ideals upon Unova, either to back up N or to come in if he failed. Just like N being a Zorua, the hybrids would be kept top secret among him, the Shadow Triad, and the scientists in on the project. But he couldn't figure out how to do it, and neither could his scientists. The scientists eventually came up with what they thought was the correct formula, and they tested it out and that's how Genesect came into the world. Everything is the same from then on, except Ghetsis's scientists were never successful in creating the solution. That's where the traitor scientist comes in. Learning from their mistakes, he independently creates a successful solution, and keeps it hidden from Team Plasma. Then he goes off and creates his own personal army of hybrids, and since at this point the fully modified Genesect already existed, Destiny would be able to be a Genesect hybrid. Plasma finds out about the hybrids, Plasma catches the scientist, Plasma obtains the formula. Bingo, Ghetsis fuses himself with Genesect. All the while, GMP649 is passed off as an ancient Pokemon that had been revived so that grunts wouldn't suspect anything when encountering Destiny, GMP649, or whatever. The end. I think everything works now, right? If not, then I'm sure there's some way to work around it. Well, so that's that. Even with the revised edition, I still don't think this would work in context with the roleplay, so it'll remain story exclusive.

# 4 - The Hybrids Were Originally Ghetsis's Idea
This one heavily ties in with the twist above. Y'know what? I probably don't even have to explain this one. I think the previous twist did that job well enough, although it didn't really go in depth. But because I'm lazy, you're just going to have to deal. >:\

With that, the Plasma's Folly roleplay is officially closed, and we won't be bringing it back. Now we'll start up either Z's Academy or Legendary Genesis again, and we'll also resume working on the Omicia Project. I'll also continue working on the fanfiction.