Hello everyone, the name's Cory of PRIVATE Corp, and I welcome you all to my next big epic… and I guarantee you that this will be an epic if you ever read one.

Now for the longest time this has been bouncing around in my head and it has gone through so many different ideas, both strange and awesome, and ever since I have pitched the idea elsewhere to see what kind of reception I get. So far… it was stupid. But now here in a time where I made two successful fan-fics based off completely two radically different ideas and then shifting into a show-hopping epic of a crossover that takes the original concept of that pair and spins it on its head, I am here to bring you a new venture into my work by writing a story that's a part of my childhood ever since the first generation and I'm still a dedicated fan no matter what goes on in the games.

It's the return and rise of Cipher as an evil world organization.

Now I know there are stories out there that have writers taking Cipher and getting them back in the limelight, with Ardos leading the charge, but I feel like I can bring something new to the table. And really, what can I do other than having Ardos taking over what his father failed to do, go after legendary Pokémon and create the XD Project so that it can't be destroyed or fail because some unknown Trainer from a small town in the country decided to get involve and save the day by capturing all of the Shadow Pokémon and stop the most corruptible and irreversible Pokémon from destroying all life on their world?

Well… let's find out, shall we?

Legal Notes: I DO NOT own the Pokémon series. All of the strange creatures and the world they inhabit are owned by Game Freak, while any music that appears in this story is owned by their original creators and any original content is credited by me, Cory of PRIVATE Corp, or any guest creators.


Prologue – Awake the Shadows

"No matter how hard one fight to rid of them, shadows will exist. Good or evil, the shadows are a part of us."

OOO

Pokémon: creatures of unknown origins. These mystical creatures have lived alongside humans throughout the birth of civilization, even existing long before human beings were created. They are fantastic beings; many and many species of varying shapes and sizes are observed and recorded, while there are countless out there that are waiting to be discover. These creatures occupy many parts of the world, from the highest mountains to the deepest parts of the ocean; there is no shortage of Pokémon for people to find.

And even with the countless individual Pokémon roaming the planet, there are a few that make up legends. These powerful Pokémon were said to shape the planet, universe and gave life to everything, creating legends that continue to fascinate generations to come. Hardly anyone knows what these Pokémon are, how many exists now and before, or what created them, but this desire to teach pushed people to study more about these creatures and the legends surrounding them.

Humans and Pokémon alike have grown over the countless years, with them fighting each other during periods of war. Before long, the two sides overcame their hate and joining together in various partnerships. These bonds became a trust, a friendship, in where in rough times one side would come in aid and help push the other in the right direction. Over time, the bond created by both Pokémon and humans helped shape the world that we all know today.

And then there are those who use their Pokémon for evil. Villainous organizations and groups rose up and did all sort of malevolent schemes, stealing Pokémon and corrupting them to perform the same wicked action their human Trainers were performing. These groups used different methods to get their Pokémon and to accomplish their tasks, whatever it may be stealing, kidnapping or other means of force. Whatever goals they set, they will use everything they can use to achieve their dark and twisted dreams.

But even with the dark comes the good. Pokémon Trainers from far and wide go out into the world and get involved in these evil schemes, putting an end to them before they can complete it. While these Trainers started out on a simple goal, these unexpected turns of events pushed them to become heroes of their regions. Even if it was nothing to them or something they never dream of, there are Trainers that will prove themselves whenever evil rises up from the darkness.

This begins the story of five individuals all starting out on their own Pokémon journey, all unaware that they're about to get involve in a large plot. There will be many hardships, as well as countless faces both friend and foe, but in the end they will come together and join forces to put a stop to the world's largest operation. This is their tale, and how it call began in the darkest part of the world…

Welcome to the world of Pokémon!

OOO

There was something sinister hidden about out at ocean. A few lingering storm clouds rolled across the brewing watery surface, bringing around pockets of rain waiting to drop and lightning charging up inside. Waves were unpredictable, stretching out wide and high to prevent any sort of watercraft from trekking out far. Along with the waves, there were whirlpools dotting the watery surfaces, spiraling down to the drowned earth deep below. It certainly was a bad part of the ocean for anyone to venture out in, but there were some brave souls hiding in the midst of the stormy chaos.

Out in the middle of the dark patch of the ocean, a gloomy island sat isolated and far from human contact. Its rocky surface lacked any sign of life, no patches of green, only a mix of reds, browns and greys that made up the island. Rising up to the dark heavens, a volcano steadily streamed rivers of lava out and down to the murky ocean, slowly forming new land and lifting the island higher up. And hovering above a pool, being hold up by the strongest of steel beams was a large metallic sphere, housing hundreds of workers slaving away at making repairs to the sphere.

In fact, the steel sphere wasn't the only building on that island. Deep below the rocks and hidden in the magma pockets and water surface was a spider web-like network of corridors and hallways. This network made its way out to where some of the whirlpools were and in certain clear spots, with rooms placed there to create currents and deterred unwanted visitors. Much of what was known about the island, its sole building and the network underwater was kept hidden, except for those who were currently on the island.

Covering every inch of the island, above and below it, men and women dressed in a silver uniform were performing various tasks. A lot of these men and women looked nearly identical from each other, since their uniform were all exact, with the only differences being their body structures and gender. All of these uniformed members were doing something productive, either working with creatures of various origins or slaving away at the elaborate base.

Somewhere in one of the many hallways, two large bodybuilder-like men were tailing a tall shady character dressed in blue. He casually made his way through the hallway, passing by some peons and each one of these peons either gave a salute or a brief moment of shock. Despite the man's unusual appearance, he possessed tremendous power and all of those dressed in uniform knew this. Even without the two guards by his side, they wouldn't bothered messing with him due to his connections, his past, and what he has at his belt. The man stopped his guards at a door, telling them to wait as the man opened the door to visit whoever was inside.

First up, it was a small little office painted very similarity to the rest of the facility. Along the walls were several sheets of paper, mainly newspaper articles and snippets, along with many faces of several different individuals. Right on top of each sheet was several strings of various colors pinned down into the pictures and articles, linking together to form a network only fantasized by even the craziest of conspiracy fanatics dream of. All of these strings were meeting up at one large map of the world hanging up on the opposite end of the world, creating a rainbow blooming from various regions on the map.

However instead of some insane conspiracy theorist, sitting at a desk was a regal woman reading a local newspaper. Her knee-high red boot covered legs were crossed, with the rest of her legs covered up by a knee-length pink skirt. Flipping through the pages were a pair of dainty fingers, hiding underneath orange sleeves with fire stripes wrapping around. There were peeks of a pink top with gold trimmings and a small window revealing her large breasts, but only when she closed the newspaper to change pages.

The man in blue made his way up to the reading woman, and she folded down half of her paper to see who was in her room. She gave the blue man a cold gaze, staring at him with her deep purple eyes, and her eyebrows were arched in to make a quizzical look. Draped across her face was a strand of vanilla blonde hair, compared to her puffed-out chocolate brown hair draping down her back.

Without saying a word, the woman knew what the man was going to ask for, and she folded up her newspaper and got up from her seat to join him. The two of them made their way out of the office and on down the hallway. The regal woman commented on why the man needed two bodyguards when he himself was formerly one, only to get silence from her superior. The two spent the new few minutes in silence, making their way through the network before stopping at another door.

The next stop was a larger room, holding various machines and different pieces of technology. Working inside are the few individuals not dressed in the silver armor, instead opting for more of a mad scientist appearance, and many of these scientists were slaving at the machines to get them to work or maintaining them to prevent failures. There was a strange smell in the room and an alarm, prompting the scientists in the room to stop what they were doing and rush to solve the problem. But they were late, as a large flume of smoke started to fill up the room, and a slew of curses were coming from a deep voice.

Stepping out from the cloud was a tall man, roughly a head taller than the man in blue. His attire was almost like the others in the room, save for his color scheme was a mix of blue and brown, and he had more stripes than the others. His coat was reaching down to his feet, covering up his purple pants and whatever was hiding for a shirt, while his lavender gloved hands were fanning away the cloud to clear his vision. There were also belts hanging off of the man, with two dangling from his shoulder and two wrapped around his waist, with one of the waist belts containing six identical ball-like capsules.

As soon as the smoke cleared, the man noticed his superior in the room and he gave a serious stern look and a small salute. On the man's face was a pair of blue-framed glasses, but to everyone they couldn't see what was resting behind the one-way lenses. Even if they couldn't see the rare glimpse of his hazel eyes, there was a sense of coldness coming from behind the glasses. His black hair was stylized to point straight out, leaving a flat surface to allow anything to sit on top, while his forehead was showing off a widow's peak to allow his narrow eyebrows room to emote.

The man in blue questioned what happened that caused the explosion, getting a brief answer from the scientist. There wasn't a further response from the man in blue, which the scientist was taking that he must not allow that to happen again. The superior man motioned for the scientist to leave the room, before he ordered the other scientists to fix the repairs and continued on with their work. The scientist in blue joined alongside the regal woman, the two discussing ideas between the two, as the three of them continued on venturing the halls to the next room.

Their third stop was a gym, specially made for those who classified themselves as bodybuilders. There were plenty of lower-ranked peons at the workout equipment trying to match strength with their larger counterparts. Lingering in the air was the stench of sweat, building up as the men and women continued with their plans. And in the far off corner of the room was a boxing ring set up for both humans and Pokémon, although there were only humans training in the ring at the moment. One of them got a punch to the face so hard, the man flew over the top rope and right over to the man in blue.

Standing in a ring was a young teenage girl, doing a celebratory dance to commemorate her latest defeat. The girl was definitely not like the others in the room, as her attire was more fitted to the lifestyle of the workout center, and her small lean figure has a hint of muscles on her arms and legs. Most of her body is covered up in a red spandex swimsuit, hiding underneath a light grey hoodie jacket with pink trimmings and hood, and a pair of purple boxing shorts hanging off her waist. Her hands and feet were covered in red, with a pair of training gloves on her hands and sneakers on bandaged wrapped feet.

The fallen peon slowly got back up onto his feet and he looked up to find his superior hovering above him. The peon quickly stumbled back up, apologizing for allowing such a disrespecting thing to happen. The man brushed the peon aside, making his way up to the ring before asking for the girl, a redhead, to step out to join him. She leapt over the ropes with ease, landing right in front of the man in blue, and the two of them exited the gym to join the regal woman and scientist.

Finally together, the group made their way through the halls all the way to the spherical building. Inside, they got to a large room made into a conference room, where there are three tables fitted to form one square-ish U-shape. The man in blue took one side of the table before reaching the end of the room, while the three guests walked down the middle of the tables. Once everyone was in place, the man in blue dismissed his guards, letting them guard outside while he holds his conference in private.

"Oh what a day today is," said the man in blue, a passionate smile on his face. "It's been years in the making, a chance for us to finally see through the rise of Shadow Pokémon and for me to take charge of it all."

"To be fair sir, I am the one overseeing the procedure of the Shadow XD Renewal project," the scientist commented, "but your input is most grateful in helping getting the project up and running."

"It's amazing that after all this time, everything is still here," the man in blue replied. "You think that everything would've been confiscated and be used against those caught by the police in their trials. But no, it's all here and still in working condition. Odd, isn't it?"

"It's not that hard to get those gullible policemen to fall for anything," the regal woman commented, flicking away the blonde strip of hair from her face. "Throw another scandal in their faces and they'll be scrambling to get it cover. Plus who would ever think of come out here in this condition? You have to be completely stupid to ever make the trek."

"And just look at us," the teen girl added, her hands behind her head. "We're brought several men and women out in the middle of the flipping ocean all to get some silly project going again. You gotta be outta your freaking gourd to think of something like that."

"And that's part of the reason why I've selected you three to represent the new Cipher and my goals of total world domination," said the man in blue. "It might get a little suspect if I get more recruits from around Orre, but if I want to start with a goal like the world, why not have others from the different regions?"

"Your logic is a bit sound, but it's not absolute," the scientist noted. "You may have some of the best minds, brawns and strategists hidden in the desert, but you're risking a whole lot more here recruiting from all over the world."

"Yes, but it is just a beginning, after all. Something like this hasn't truly been tested before, but what is going to stop us this time?"

None of the three could answer that question, leaving a dead silence in the room. "Of course I know there are those meddlesome Trainers that loved to stick their noses into everything. And what has come of this? The fall of Rocket, Magma, Aqua, Galactic and Plasma, twice for the latter no matter by two separate Trainers, and even our own organization has fallen twice to the same method! Well no more!"

"And what makes you think this time will be the charm?" the regal woman asked. "The police here are bound to suspect something's up and it'll be a matter of time before Interpol get involve…"

"Relax my dear, why do you think I brought you here in the first place?" the man in blue replied. "Yes dealing on a scale this large is going to attract a lot of attention, but as long we know what kind of threat stands in our way, then we'll—"

Just about as he got to finish his sentence, the doors opened up behind them and they turned to see who was joining them. The sound of footsteps echoed off the walls, an unsteady beat as if the man had a bad leg, and they all could see the man has some kind of limp underneath his robe. In fact, the man was dressed in head to toe black and various shades of grey, showing little of any other color other than his sickly white skin. A hood was draped over the man's head, covering nearly everything, and a headband was wrapped around his eyes, leaving only the lower half of his face and neck exposed. The others watched as the newcomer slowly made his way into the room, their eyes focused on what was sitting on the man's shoulder.

On the man's shoulder was a Pokémon that stood out completely against his somber appearance. It was a parakeet-like Pokémon, an odd looking one with a black head resembling a musical note. It was brightly colored with blue wings, a pink beak and eyelids, a yellow "bib" and talons, and a green stomach. Despite its colorful look, it looked as serious as the man next to it.

"Oh, I have forgotten about you. Fellow Admins, this here is Tacitus," said the man in blue. "He's the representative Admin for the Unova region, and he's… not exactly a sound man.

"I'll say," said the teen, looking at the cloaked man with a dirty look. "Why do we need some crotchety old man on the brink of breaking a bone, and what's up with the Chatot?"

"Don't doubt the man's current state," the blue man replied. "He knows a lot when it comes to Pokémon, especially with unlocking their true power. I don't know much about his condition, other than he's not well enough to speak, so the Chatot was given to him to help aim him aid in his speaking."

"Yes and what makes you think we can trust you, little brat?" a rough voice asked, coming from the bird.

"So your Chatot is speaking everything for you?" the scientist asked, getting a nod from the bird. "I never have seen such an occurrence before. You must be very smart into figuring out your Trainer is saying, Chatot."

"I may be, but I'm more than some simple translator," the Pokémon replied. "Anyway, we would like to inform you that there are some suspicions going around about a spy in the ranks, possibly someone disguising themselves as a peon."

"Already?" the man in blue growled. The man thought over what to do next, thinking over what sort of action is suited. "Well, what can you do? Seal the island and have peons look out for any suspicious activities. If they spot anything, use whatever action is necessary to prevent that spy from leaving."

The cloaked man and his Chatot returned a bow before turning away from the group to head out. As soon he got to the doors, they opened up for him without so much him touching them, as if it was planned. The cloaked man left the room the same way he entered, all without a word, and the doors closed on the group once again with the three Admin just who was that man.

"Sir, are you certain we should have this man be a part of our ranks?" the scientist asked, sounding a bit worried. "There's nothing we know about the man, besides his abrupt introduction."

"And I trust you as equally as him?" the man in blue questioned, his eyes narrowing on the three Admins behind his glasses. "I hold no value in any of you until you can prove yourself. Otherwise there is a spot for all three of you that I consider to be completely trustworthy…"

The three Admins were confused as to what the man was suggesting, looking at his cold emotionless face in hopes of finding something. After a few minutes, they realized what he was getting at, and all three of them lost color to their faces.

"Now, now, I won't easily drop you after I spent months searching the world seeking only the best of the best to represent me and for all of Cipher. I can't let you go because I need your services, expertise and Pokémon knowledge if we were ever to get Cipher out and ruling this world.

"Young Matilda, despite what many have said about you, your spunky attitude and fiery spirit has proven useful in my operations. Your fighting style may not be suited for humans, but perfect for snagging as well fighting Pokémon one-on-one. In fact I could call you a Pokémon yourself if the situation calls for it.

"Cato, you may not have much knowledge with our operations, but you know very much into how a Pokémon works and what it'll take to seal its heart to form the perfect Shadow Pokémon. In fact, if what I heard about this ability you have, you could be useful in making the ultimate Pokémon weapon.

"And the beautiful Maysun, while you possess the looks needed to attract many to our way, your brain is the most beautiful. Wonder untapped information about the underground operations, various organizations and just about everything needed to know who is for or against up, all waiting to be unleash from that mind. I cannot begin to imagine what kinds of secrets are being held inside.

"And together with Tacitus's knowledge of everything Pokémon, we will have the rise of power Cipher has been seeking ever since its creation. We'll make sure that this happens and I will be damned if anything gets in our way again!"

The three Admins were in agreement with the man's little speech and they applauded to help fuel his pride. Just as they were wrapping it up, a screen appeared on the . "Sir, we have located the imposter and we're on the move to prevent him from escaping," the peon stated. "However it's proving to be difficult to apprehend the imposter."

"Then use force if you have to!" ordered the man in blue, slamming his hand onto the table. "Make sure that whatever they're doing doesn't leave this island!"

"Roger that!"

The man in blue straightened himself out as the screen on the table disappeared, and he looked towards the redhead, who was eager about what she was going to hear. "Matilda, go help out the peons," he commanded. "Help them in the physical department if the intruder is proving to be difficult."

"Right!" the teen girl replied, giving a salute before making her way to the door.

The doors were kicked open by the little girl, frightening the guards on the other end, and the doors shut back in place, leaving the man in blue to look at the other Admins left. "Cato, return to the labs and continue on with repairing the machines," he ordered, getting a nod from the scientist. "Maysun, continue on completing that whitelist so we can start sending peons out to the other regions to begin our operation."

Both Admins made their way out of the conference room and they went in opposite directions to tend to their jobs. The man in blue turned around to look out at the world, seeing the dreary dark ocean surrounding the island. After a few minutes, he made his way to the doors and he got his guards to follow him, all in the intent to deal with the intruder personally. One way or another, whoever it was, they were going to make it to the only exit on the island and he wanted to get there before the intruder does.

All around peons were running back and forth, wondering where in the facility is the intruder. Some of them were questioning each other as all of them look all identical from one from another. This was going to take forever if all of them are asking to remove their outfits and interrogate them on the spot. One peon shouted that they found the intruder out by the shoreline, and the man found his way outside to find several peons in battle position, and a large floating blue ship with something on top.

Out in the ocean, there was a boat looking much like a large sea Pokémon, and standing on top of it was the culprit. From what they could make out, it was some bipedal fox-like Pokémon, grayish-brown in coloration with crimson and black accents, which would've been impossible to make out if the boat wasn't bright blue. Its back was turned to the people, letting them look at its large, voluminous mane tips. They could also make out the arms and legs of the creature, standing proud and holding the disk in one of its claws.

The Pokémon looked back at the facility, especially up at the dome, and it gave a snickering grin. It presented the disk to the group for a final viewing before a hatch opened up and the Pokémon jumped on down. A few of the peons grabbed some of the capsules by their side and prepared to throw them, but their superior stopped them, preventing them from risking their teams on a wasted effort. All of them watched the ship sink under, heading off into the unknown and passing by the defenses of the island.

"Was that a Zoroark?" the man in blue asked.

"I believe it was, sir," answered one of the peons "Should we go after it?"

The group waited in silence for their superior's next order, anticipating on what he was planning. The man in blue turned around and started heading back into the facility, leaving the peons wondering why he was doing this. They decided on to follow their superior, heading on back into the facility to continue on with their previous tasks and wait for their next orders.

However, the man in blue reached out and grabbed one member on the shoulder, pulling him back so he can speak with the peon. "May I have a word with you?"

"Uh, yes s-sir?"

"Gather all of the peons. We need to discuss our new uniform policy…"


And finally this story lives!

All right, now I am excited about the new Pokémon X and Y coming out, but sadly I already added two regions during the creation of this, especially with one that really changed things for me (Generation V), so I won't be adding the new games to this story. I might, however, have some of the new Pokémon appear in this story… once more appear.

So, as I mentioned in the first chapter in A Cinnabar Nudist's Story, this here will be focusing more on the games than anything else, but I do want to combine elements from the other mediums to create a great broth of references. Of course this will focus more on the games than not, I still want to blend everything into this sweet broth of fan-service goodness. And I'll also take it into moderation as well.

Also I find it odd that while this is a first time that I'm doing a mute character, I'm getting the reference wrong. Don't get me wrong, Tacitus is a reference to Rob Lucci, but I find it strange that I'm using a Chatot instead of a Pidove. Then again, considering that Chatot is the only bird Pokémon that can speak like a human, it's the only thing I got. I really doubt I can somehow justify a human-speaking Pidove in anyway (there's no way Chatter can be bred to any Pokémon, right? Why haven't we got an Meowth that knows that?)

But enough about our silent Admin, who's excited about seeing Cipher back in action? Well sadly we ain't gonna see them in a while… aww. Now this is roughly I haven't got anything at this point, but then again it's not like I'm going to jump right in with their plans. It takes time to build. But I do promise that we will get to see them in action, whether it's through the new field agents or maybe an Admin. And I can say to you that we will see returning faces from Orre, including one smug traveler that was annoying in the past (to some anyway)…

Also I would like to point out: I read every single entry in the Evil Overlord List. If Cipher isn't already dangerously genre savvy at this point, they will hit the peak when time comes for them to really shine.

And finally, I really want to incorporate music into this. I'll probably put a note in the beginning of the first chapter to the Kanto storyline, but I'll let you know about what song goes where (since apparently I can't add HTMLs in stories. And I want to make this story better…)

So for now I would like for you to review, thank you very much. Coming up next: The first chapter of the Book of Kanto, the start of two boys' journeys into becoming Pokémon Masters, and play that funky music white boy!