Woah, its been ages since I even thought of writing a new story! This is the first in a possible trilogy and a story I've had cooking for a while now. I really hope people enjoy it as much as I did coming up with the ideas and I hope I don't disappoint and actually manage to keep with writing, eheh...

Disclaimer: I do not own any content related to the original Pokémon series, species, anime or anything along those lines, this is written by the fans for the fans.

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Chapter one:
Tutor

"Come on, look this way just once... Give me something to at least pretend you're looking at me, like I actually exist to you."
No such luck it seemed, as the hot brunette chick that sat across the room from him every morning ignored his pleas and carried on typing, oblivious to his intentions, at her desk. Or maybe she wasn't oblivious, but more than likely knew as well as he did that a total nerd loser, not even fully fledged scientist rather a college graduate assistant, had absolutely no chance with someone like her.

Andrew sighed deeply from his small, unkempt desk (which for being his supposed 'work station' he actually spent very little time at while on the job) the sound not so much as even causing the spectacled secretary to blink, much less get her attentions. Heck, even if he was earning around ten times more salary than her on this project, she was still out of his league. Ruffling his unkempt red hair awkwardly and accepting both his defeat and yet another bruise to his pride, the young man grabbed his files and card passes from one of the drawers and made his way, unsuccessful, out of the room.

"Tomorrow is another day. And the day after that... and the one after that." He attempted to reassure himself, only to fail miserably. Not that the secretary actually meant that much to him, but he more saw it as a kind of challenge to get her attentions, perhaps even her interest.
Not that it would ever happen. This was a shame, since he was a terrible sore loser, despite how much losing came naturally to him and he knew very well he'd be nursing a wounded pride for a long while afterwards. In a place like this though, it was only natural for a guy like him to make little games out of normal things for entertainment, or merely for a small pick-me-up despite his numerous failures. The seriousness of the entire place was intoxicating if you let it get a hold of you.

"It's an underground government base. Not exactly on the top ten list for relaxation." He reminded himself, purposefully not adding on the small fact that it was, of course, under rocket control.
People weren't aware of it, but pretty much most divisions of the government were run by those sympathetic to the renegade organisations cause. Of course, they didn't do anything public these days. The world remembered rocket of simpler times as a mild threat at the time, but ultimately failure of a team. By working secretly, it was so much easier to get things done and things even became acceptable to the public eye as long as they were portrayed just so and their grisly truth hidden. The original group had gotten it entirely wrong with being so brash and open, given that the underground re-incarnation had flourished upon its revival and under new guidance.

Not that he was particularly into the group and its ideas or anything. At least, he had honestly never intended to end up deeply involved with the team, much less on one of its top projects. But when he had been approached after his graduation (he'd apparently excelled in his area and had been just the kind of person that 'they needed') and offered a salary and secure future that he could only hope for after nothing short of a miracle and some serious time spent in one of the region's top universities, which to be frank, he couldn't afford.
Of course he accepted to enlist with them, no strings attached.

And to be perfectly honest, it wasn't as bad as they made out. The members didn't go around stealing children's teddy bears or kicking puppies, which was the general image that came into one's mind when thinking of the illegal group. They were actually quite friendly and, to Andrew's surprise, mostly as normal as he was. Of course there were a few generic wack-o's (such as a certain Dr. Strothe) but that was just natural in any work-place with such a large amount of employed staff. If you could handle the idea that you were technically working for an outlaw organisation (although as the better part of the government, were they really 'outlaws' so to speak?) it was a pretty sweet situation to be in. The pay was amazing, directly funded from the government and you were pretty much guaranteed a cushy future for your services.
If you kept your mouth shut and were obedient, at least.

That and you had to be pretty open minded. Not just about the projects and work itself, but about living arrangements. This particular base, the main and largest, was situated some ridiculous mileage underground a remote island off the coast of Vermillion bay. Living quarters took up a large space for it, as all staff from the top dogs to cleaners were required to live on-site. The quarters themselves were pretty nice, devised into different 'sectors' each with its own snappy name in honour of a particular tree, something which you didn't see this far underground so therefore was rather pointless to Andrew. It was cramped, yes, with the rooms consisting of a single room for your bed, desk, belongings and whatnot and a small bathroom. Entertainment was to be found in the 'communal area' of the particular tree's legacy and food was to be consumed in one of the many restaurant like cafeterias.

All of this was around seven and eight stories underground, enough to give anyone cabin, or in this case 'underground base' fever. Not that Andrew liked the living quarters much. The people he was fine with, even if he mostly kept to himself around them, but he found the place as high tech, spacey and futuristic as it was, dull in comparison with what lay even lower underneath the earths surface.

The only way to access 'the cage', as it was so fondly nicknamed in these parts, was via an elevator system. Huge, ridiculously touchy machines that travelled the last few miles down to the very bottom of the base and with more security installed on their mainframe than a large bank. There were about four of these, which was somewhat impractical for the amount of usage they faced, but for some reason such a small number was viewed as 'safer'.
"Bullshit." The young man mumbled as he reached a hand towards the caller button and withdrew an access pass from within a lab-coat pocket. He decided the higher ups just did this to laugh at everyone as they squeezed inside the tiny boxes, happy at being able to avoid this prospect given the elevator that opened to him was empty.
Well, it was 6am.

He couldn't help but groan as the huge silver doors closed and then a robotic female voice announced, cheerily of course, that it was going to perform a bio-scan on his persons, just in case he was one of them and decided to go BACK to where he came from rather than proceeding further to freedom. Of course.
The ride down, was as always, painfully slow. Not that the elevators themselves were slow, they were actually quite zippy things, rather the decent they made being incredibly steep. This was one safety precaution Andrew agreed with though.

ID cards clicking as they collided around his neck upon every step he made, the young assistant eagerly made his way out of the elevator and into the purely silver, metallic corridor. The floor clinked under his steps, leading him towards the eventual end of the corridor and a huge metallic door. The structure itself was at least as three times as tall as Andrew, undeniably a bunker door, though in this case 'seal' would of been more accurate.
Apparently used to and entirely un-awed by the sight, he made his way towards a small terminal with a camera stationed towards it and mic.
"Morning, Kristy. Mind giving me access a little earlier than normal? I left earlier expecting to get breakfast but then decided not to bother." After a few moments of static, a clearly female and surprisingly gentle voice replied.
"Sure thing, most of the group are still sleeping anyway so you shouldn't disturb them. All accept your one, of course. That thing always seems to know when someone's coming to visit... Anyway, you know the drill, swipe your card and go through."

Seconds later, in a scene from a sci-fi movie, the huge doors burst to life in order to grant him passage. Again, he seemed unimpressed and made his way inside, pressing a button on the other side to close and seal the doors once more. He was instantly submerged in greenery.
'The cage' wasn't exactly a cage so much as a huge dome. Or rather, home to the bases current pride and joy, not to mention latest scientific breakthrough. For a pen, it was actually quite pleasant, being filled with all kinds of greenery, and artificial enhancements that imitated the outside world. Not that the specimens knew what the place was actually like. 'The Cage' was shaped like a huge dome, with the staff area being shaped like a huge inner-tube around it so that they were able to observe inside.

They of course entered with them sometimes, just like he was about to. He actually considered the cage to be one of the nicest places on the base, what with its lush environments not to mention the artificial sky that hung over it. A lot of people actually came here off duty to simply feel more at home, as odd as that was.
Andrew couldn't help but laugh slightly at his sudden realisation. The most human friendly habitat in this total place belonged to the creatures that weren't. With a sigh, he made his way into the dome and the domain of the creations.

After just a few paces, he came face to face with talons, flashes of wings and horns. Claws, teeth, tails and spikes surrounded him, yet he remained completely calm. The creatures which the appendages and features belonged to seemed to flock around him, slowly moving closer. Mostly humanoid in shape, but pained in fur and skin every colour of the rainbow, some with feathers, some with scales. Inhuman. One made its way towards him, long claws outstretched and striking magenta feathers streaming from the side of a face.
"Good morning, Red." The creature politely greeted, to which Andrew smiled at the Sneasel hybrid, before sighing once more, but still with a grin.
"Geez, how many times do I have to tell you early birds, its Andrew?" He groaned, to which the exotic creatures all seemed to chuckle at or smile. The assistant looked around him and at the group, noting that it was always the same group that was up this early. Mostly the normal types, given they were nearly always bouncy. Not that it mattered much.
"Any of you know where my girl is?" He asked shortly afterwards, to which the sneasel male pointed his claws to the right and indicated to a small grassy area with a pond.
"Should of guessed." Andrew mused, before giving the creatures a faint wave and automatically excusing himself. It only took him a few paces to reach the pond, his girl's particular favourite spot to simply sit and amuse herself. As always, she was humming, a husky melancholic tune this time around. She seemed dazed when he approached her, but as soon as she noticed his presence, perked up.
Large, impaling blue spikes protruded from her back and shielded red eyes, along with a particularly nasty pair from her long tail. Sleek purple skin clashed with bright blue scales, arms reaching upwards to his face in greeting not with hands, but large, finger like feathers, useless for basic handling of objects.

"Good morning, zero. Enjoying the pond?"
He didn't expect her to answer. Any question beyond her name or how she was completely out mastered her, nor did she know many words other than those that were simple and were used frequently to perform basic sentences.
Not that she was dumb. Just she hadn't been designed to be all that knowledgeable in things that weren't seen as necessary for her purpose.
Which as the crowning gem of the biological weapon project wasn't all that much. She was dangerous, a high tech 'machine' almost, designed to kill and obliterate easily. A living creature capable of unleashing the equivalent of a nuclear air strike upon the world.
And he was its tutor, not to mention found her actually rather sweet.
Naturally, with this in mind it wasn't much of a surprise that she hadn't been designed excel in the English language. Still, he could only try his best, removing the toddler book from his files with different shades of colours in it.
"Red." He began, pointing at the square of colour represented by an apple. "This is red. Try and say Red?"
Oh yeah. He was totally on his way to being a revolutionary scientist. One colour at a time.