Series by Croft.
Story prompt for Five Nights at Oak's 2:
"It's got to be here somewhere. I know I stuck the backup file here somewhere. I just need to find it."
Somewhere in a dark and largely abandoned facility built into a sloping mountainside, a single figure bathed in dim light and shadow worked sifting through piles of discarded, broken and dusty machinery with a weak light at his side. His voice was raspy and wise, the sort of voice that had sent dozens and dozens of 10 year old children on world-spanning dangerous adventures. He lifted himself and wiped his sweat stained brow. "Oh how did all this go so wrong? It was meant to save the world, to bridge the gap between pokemon and man. This isn't what I wanted. This isn't what I wanted at all. I must find that backup file disk. I must!"
It had been nearly just long enough for the incident to go out of public mind. The public outcry and terror as people of all walks had been forcibly turned into shapely and attractive latex facsimile of pokemon from across every region of the known world. Man, women, furry, no one was spared the treatment of being abducted in the middle of the night to be forcefully encased in rubber suits that imitated Arcanines, Espeon, Charizard, and every kind of pokemon known. It was given multiple names by news outlets trying to quantify what had happened, but in the end it like everything else in the news was forgotten. The victim's had all been freed, and though some had suffered psychological trauma, most all were fine in the end. Was it true that there was now whole insane asylums occupied by rubber obsessed people who only knew how to communicate by saying "Char! Charmander Char!" or "Pi-pika pika! Chuuu!" ...well yes. But they were a minority. The various police forces who'd all worked together to stop the rubbery madness had never been able to find the mastermind though, whom they all thought was sweet old Professor Oak. For that matter, they were never able to find Professor Oak, as he'd gone missing all those months ago, never to be seen. This had all happened so long ago that it was nearly forgotten. People would soon wish they'd remembered it. Then they might have been prepared for what was to come.
"Oh where is it... I know it has to be here, it simply must be!" The old man stumbled as his lab-coat pocket square vibrated. He stumped his toe as he accidentally kicked a turned over filing cabinet in surprise. A thin rectangle of metal fell onto the floor from his pocket square and vibrated.
"ME AND YOU AND PICACHU! FOUGHT THE WAR, FOUGHT THE" - *BeeP* "Hello? Oh... yes Red, it's been a while. Look I'm sorry I don't have time. There's something I'm doing here and...what? You mean it's started? But but that's. That doesn't. Ok. Yes, I know, just stay indoors. Try and keep your mother safe. Be careful around any pokemon you see, it might be a rubber suit pokemon in disguise. I'm almost certain that I'm just moments away from finding the disc, and then this will all be over. Yes yes, take care." *BeeP*
"Oh that boy... Always my star pupil Red." Oak put the phone back into his labcoat pocket, and continued sifting through the rubble. He was so consumed now with his urgent search, he didn't hear what was coming up behind him. "Gah! Wh-wh-what!" A rubber Rhydon had grabbed him with it's two large shiny arms, and bear-hugged him into submission. "Let me go this instance! I demand-!"
"You're in no position to demand anything... Gramps." In the darkness the voice could have come from anywhere beyond Oak's weak lamplight, but who owned the voice was unmistakable.
"Oh no...it's you. How could you do this?! We hmmmppph- mmph-" The Professor's outcry was cut into muffled silence as the Rhydon holding him immobile placed it's smooth slick surfaced palm on Oak's face.
"How could I? How could I...that's almost a good question Gramps. But the better question is how could I not?" The voice from the darkness echoed all around Oak who was now struggling furiously with no headway being made. "You see Gramps, soon my latexified pokemon will bring me...subjects. And these subjects will become the first of a new breed of pokemon. The second they're inside these new pokesuits, they'll be physically stimulated, mentally hypnotized, and conditioned until they might as well be those pokemon. Then...then the next phase starts. And I want you to be there to see it all."
"Mmmm mmmm mmplah! You won't get away with this! I'll get- mmmh mmmph!" The old professor broke free only to deliver a failed and moot threat, and his captor knew it.
"Shhh...quiet now Professor Oak. You've got...oh lets say...5 days. In 5 days everything will be in place, and then your lofty dreams of coexistence between Pokemon and everyone else...well that brings about the end of the world, and the start of something much better."
Source: http://www.furaffinity.net/journal/8275145/
Note: this pool is currently incomplete, feel free to add to it.