Pokemon Paradox Prologue

He knew of the Cipher project to create the ultimate shadow pokemon by extracting Latios' genetic material via electromagnetic energy from Altomare's soul dew. He knew all the technology invested in the project, all the time and effort put into it. The programming and injection of nanobots, the usage and development of nanobacteria, the painstaking task of negating all capture devices- including snag balls- as well as immunity to status and battle effects, diseases, and toxins, rapid self-healing and regeneration, immunity to psychic holds, ghostly possession, and mental confusion, and the ability to utilize aura manipulation. He knew of the fatal unforeseen mishap in the final stage and step of the project, how someone had infiltrated the computer mainframe, shut off the power, and consequently freed the latios as it was being injected with the shadow formula. The result was the rampage of a latios with a deteriorating mind and soul. Currently, this latios was an empty, soulless shell infused with shadow energy and a damaged nervous system caused by everything injected into him. This latios would be the centerpiece of  Project Paradox.

"All subjects have been acquired." A calm and collected voice spoke from the artificial intelligence programmed into the system. "Anything else required, Charley?"

The man, Charley, nodded. "My Xatu predicted some suitable subjects will appear through an inter-universal disturbance shortly. I request that they be subdued and brought into the chamber."

"Understood."

"By the way," Charley started, "Any updates on the other subjects, Sally?"

Sally answered, "The latios is in stable condition, and the genetically imbued and injected shadow energy have settled to the point of relatively safe, cooperative state. It will not affect any of the other individuals in Paradox."

An image of one of the subjects appeared onscreen. "The egg will hatch before, if not during, the initiation. Even if it doesn't, it will still be safe to continue operations. Readings show that it is a healthy male skarmory."

"Healthy indeed."

"Quite." Sally continued with another image, an expectant mother flygon absentmindedly stroking her stomach, whispering fearfully to herself. "The flygon, though prone to stress somewhat above the norm, appears to be healthy physically, but is mentally heartbroken and fragile. Reprogramming may be required for her because, sadly, her child will not survive the project."

"What a shame…"

The image switched to a trio of pokemon, a blaziken, typhlosion, and porygon-z, arguing with each other is surprisingly fluent English. "These three, which your Xatu correctly predicted would appear, came through a disturbance, ironically, with  the other subjects just mere minutes ago before the portal closed in on itself, appear to have an undeniably high IQ for their species, if not record-breaking. Astonishingly, the porygon-z appears to be housing a human mind which has canceled out any abnormalities normally found in the species. Not to mention it has some top-notch internal hardware."

Charley chuckled. "Don't get any ideas, now, Sally."

"You're the wise guy who programmed me." Sally retorted, though not unkindly. "The blaziken and typhlosion appear to have some interesting characteristics, both have high brain activity and usage comparable to some scientists, albeit moreso in opposite portions of the brain than each other. Apparently the typhlosion has visionary problems, probably from a mistake in evolution into a quilava. The blaziken has a highly imaginative- though perhaps too imaginative in some cases- brain."

"Probably could fix the eye problem with some genetic coding…" Mused a thoughtful Charley.

"The final subject is the often underestimated and underappreciated Ash Ketchum." An image of a bewildered raven-haired teen that all readers of this fan fiction should know (why would you be reading otherwise!?!) staring at the argument of the newcomers (and kinda creeped out by the wide-awake, non-responsive latios of a shade of purple and black he had only heard about being involved in the incident at Orre's Cipher projects that he knew to be a shadow pokemon). "He has encountered every known legendary at least once, involving several situations of life and death, heroism, and impulsive, usually poor thought-out actions, if thought out at all." Charley chuckled at the comment. "Involved in a few prophecies, a huge reserve of love and care for his friends and family, and an ability to go above and beyond expectations even in the most hopeless of situations, he is the perfect person to perform the project on."

Charley looked pleased with the info. "Good! Very good. Get them set up for Paradox. Oh, and EMP the porygon, don't want him interfering the process." He paused in thought. "Or you just stick a magnet on him."

Sally chuckled at the idea. "As you wish, Charley."

***

Ash woke up to a very loud and obnoxious- not to mention annoying- voice screaming a very off-tempo and -key version of nursery rhymes. "TWINKLE TWINKLY LITTLE STAR, HOW I WONDER- Hey, why are we tied up in a line except for that latios and the kid?"

There were groans of annoyance from the blaziken and typhlosion. "Seriously, whose idea was it to put a magnet- A MAGNET- on Polygon, anyway?!" The disgruntled (and now partially deaf) blaziken cried in exasperation about the mentally scrambled porygon-z.

"Your guess is as good as mine, Flare.." The typhlosion told the bipedal fighting bird.

"Hey Pyro," Polygon quipped, earning a grunt from the typhlosion. "What's two plus two? Wrong! It's cabbage!" Polygon laughed maniacally, earning an unintelligible comment that wasn't too friendly

A crack came from the egg in the room and out of it a newborn skarmory praised, "Reborn again! Take that, Death! Tyson Talon has come to live again once more-" He stopped short  upon inspecting his surroundings. Tied up and immobile individuals plus machinery for some currently unknown purpose equaled one thing for Tyson. "Aw FUCK! Not even five minutes old and I'm a part of some psycho experiment from a madman!"

"Writer of this fan fiction, hear thy cries of leafy spinach, for nobody can deny the POWER OF MY VEGGY!!!" Polygon, once again, laughed maniacally, earning a sweat drop from everyone in the room.

"For the love of ARCEUS, Polygon This isn't a freaking fan fiction!" Pyro yelled, having obviously lost his patience for the magnet-influenced porygon.

The flygon was obviously under a lot of stress. Having an expectant child, being betrayed by her previous trainer, and then being kidnapped for some sort of experiment all in the span of a day, it was perfectly understandable she would be a nervous wreck. It took all of her will and effort not to hyperventilate and break into hysterics, instead falling into silent tears. She had a gut feeling that her child would never live to see the light of day, let alone even get to hear it's mother's voice. The very idea was too much to bear and she began to sob, wondering why she was handed such a fate.

Ash felt a myriad of emotions. Concern and sympathy for the flygon and the sulking skarmory, confusion and bafflement from the trio arguing…still, and the latios- he flinched at the closeness of it and the empty, emotionless eyes- he was left unsure, and a little afraid, of its current state and the potential and hidden power it might have once had. He was not sure but he had a suspicion that it had more than what met the eyes...

***

"Are you ready to begin, Charley?"

"More ready than Rayquaza in an arm-wrestle with Lugia."

"Very well." The humming of machinery filled the room. "Should I do some genetic patching for minor or troubling problems before Phase Two?"

"Of course." He proceeded to watch the actions take place through one of many hidden cameras in the room. The looks of shock on their faces only lasted a mere seconds before the room was blinded with a blinding flash and a raging roar of pure energy blasting the subjects, save for Ash and the latios, and instantaneously converting their entire existence into organized, energized data. Every single part of them, whether it be mental, spiritual, physical, or anything else, was being stored and modified for Project Paradox. In a span of mere seconds, the conversion ended, leaving empty space where the others once stood.

Charley could not ignore seeing the teen's reaction. He grimaced at what Ash had to witness and what he would have to endure for the rest of his life, but he could not let personal feelings get in the way. He knew they would hate him for this, which would be the understatement of all understatements ever conceived, but he had to do it, his actions would possibly save the world from the nearby future cataclysm, which many people disregarded despite the raw evidence and warnings, actual warnings, from the Legendaries themselves. Of the staff that Charley had originally worked with, only he was left alive. He was not one to give up, even in the face of death, and, even though Ash may never forgive him, he had a world-altering duty to fulfill.

"Charley, Phase One is complete."

Charley's expression grew painful and dark. This would be the hardest part of the whole project, both in success rate and decisions. The least he could do for Ash was reconstruct his memory, specifically ones that would prevent trauma, depression, self-induced injuries, and shock that would be caused by Paradox. Normally, the mind could only be made to bury, hide, or obscure memories to the point of non-recognition, but this left them prone to being recalled by any circumstance. Paradox, however, allowed memories to be altered unrestrictedly, and the mind changed without limits. This meant that the slightest mishap could be the difference of breathing to having every muscle in the body to destroy itself in unimaginable (and horrifying) ways. Sally's programming was specially designed to work with the project and utilize its full potential with minimal risks. Additionally, Paradox had the ability to eliminate and completely remove any trace of memories.

Charley took a deep breath. "Begin Phase Two, and include mental reconstruction. Extensive mental reconstruction."

Sally noticed the stressed gravity of the message. While Sally was programmed to be a vital asset, she was granted a degree of free thought thanks to Charley. "And I am assuming you mean to include…"

He nodded. "Including that."

"You realize that, if this is successful…"

"I am aware. But it is a risk that must be taken."

Sally initiated it without a word.

Charley had to turn away as Phase Two began, causing the same experience that the others had gone through to happen to Ash. "When it's time for Phase Three, use your best judgment." There was a heartfelt silence. "And Sally…once this is all done and over with- after Phase Three- I want you to initiate a space-time self destruct. Nobody can, should, or even want to find this place even remotely intact. It would be a fatal mistake to have others discover anything. As my final words to be forever ingrained into Ash's head…" Here would be his final words, his final and most important message to the teen that he never had the chance to interact with for most his life. "Always follow your heart, no matter what happens. For with love, you will never fail."

Sally acknowledged the message and used it as the finishing touch. "Phase Two is complete. Starting Stage Three."

"Thank you, Sally…" He whispered quietly, silently taking out a photo that he kept in his desk. "If only I could've been there…"

"Charley, it was a pleasure working with you."

Charley nodded. "You too, Sally.. You too…" The screen showed only the unconscious shadow latios in the room, filled with a soul for the first time since the escape from Cipher. He ignored the screen signal the success of Paradox. Oblivious to the world around him and the lab's self-destruction countdown, Charley stared at the photo. In his final moments, Charley made a prayer to Arceus for the safety of possibly the most important person on the planet.


I love you, Ash… The countdown hit zero. …My son.