Due to the chaos and violence of WWII, Nazi scientists were unbounded by the peer review and ethical dilemmas usually surrounding highly controversial studies such as human and animal testing. One such study, labeled project “Tier”, was to develop a new kind of biological weapon, surrounding genetically mutated and powerful animals that would be used both on the frontlines and to police domestic territories. It would have been a game changer in the war. For whatever reason these scientists were unable to complete their work before the Allies took Berlin, and the research was reportedly lost.

Sixty years later, Professor Oak is contacted by a top secret U.S. research agency for the chance of a lifetime. He is to do research and coordinate a project by the code name of “Pokemon.” Though apprehensive at first about what his research would be used for, his curiosity had been piqued. It wasn’t just a research, they were manipulating DNA to make a fully functioning, living animal, and he couldn’t resist. He signed on. Much of the groundwork had been laid for him by some previous scientists his bosses refused to reveal the identity of. Research continued for the next five years until finally they had done it. Using the template of the previous research, Oak and his team made a couple modifications to strengthen the designs set before them. It was a success. They had created a pokemon, dubbed Mewtwo, as the successor to the failed Mew from the prior research. Everything had changed now that they created a real live pokemon. All of a sudden their team tripled in size, and they were given access to anything they needed to continue their research.

It was when Oak found a tattered journal among the many files of the previous research that he learned the nature of his research. It was a journal log of the original Nazi research. The original animal was to be created as a weapon for the Nazi Regime; it wasn’t a far leap before he realized this new animal would also be used as a weapon. He immediately halted his research, refusing to continue stabilizing an animal that would only be used as a weapon by the military. When he was told he couldn’t stop his research he disappeared entirely.

Four years later, as a student at a top research university, you are recruited by your teacher, Professor Birch, for a summer internship abroad to study a rare and unobserved animal in South-East Asia. You leave tomorrow.

Plot:
You and a group of students will go with Birch on this summer internship. When you land in SE Asia (not sure where yet), Birch will soon after introduce you to a hidden Professor Oak. The two will reveal that the real reason you all are here is because Oak has identified the location of Mew, the original Pokemon experiment, once thought to have failed.

The rest I don’t want to reveal, as it will make for a more interesting plot should this ever get off the ground. As I’m sure you’re wondering, you will eventually get your own Pokemon to battle with (this wouldn’t be a pokemon RP without some battles!), though it would only be one as the poke-ball technology hasn't been developed.

Backstory:

In a medieval world the whole idea of owning and controlling a pokemon would significantly change society. Status would be determined based upon what pokemon you have (if you have one at all), and how powerful it is compared to other pokemon. Further, protection from those who would do you harm, in a world where you not only have to worry about swords and bows but also beasts with unimaginable powers, becomes even more tantamount. While a number of different directions can be taken with this, the one I have come up with is as follows:

In a land similar to medieval Europe, pokemon are rare and powerful creatures. They live alongside normal animals (deer, bears, squirrels, ect), and are almost never seen in the wild. Most pokemon (seen by humans at least) are held by the Nobility, the Clergy, and their Knights. Because of the powers pokemon possess, their strength relative to others in the realm is fundamental to social status. Kings and hold the most powerful pokemon (Starters like Charzard, or super rare and/or powerful like Evee or Garados), while dukes, counts, clergymen, and barons hold less powerful ones (Something like a Poochena or an evolved form of something more common like a Pigeot), and finally Knights who have ones considered common in pokemon lore (think Zigzagoon and Pidgey). Social status is maintained by breeding these pokemon with other pokemon of the same species at the same social status as your own (usually with those families you intend to marry your children into), and giving the egg to the heir to your dynasty. Because of the controlled way in which pokemon are bred, it is very unlikely that someone who isn’t part of the nobility could ever rise to become part of it. Similarly, if a noble tries to excessively breed his pokemon beyond what’s necessary, he is likely to be reprimanded by his liege, and his pokemon confiscated and usually killed. In this way, society has stabilized into something similar to the feudal system of Europe.

Outside the Kings and Nobility, the Church is the other main group that owns pokemon, but use them more in spiritual pursuits rather than fighting (most church pokemon are psychic type). The Pope, head of the church and representative of God on earth, is the only human to hold a legendary pokemon: Mew.

Plot:
Just like in real life, not everyone follows the established order. Bandits and other lawbreakers as well as mercenary bands somehow have managed to get a hold of pokemon of their own, and use them to their own ends. It is with one of these mercenary groups, the Trainers, that you find yourselves. The Trainers are different than other groups in that they only take jobs in which they believe the cause morally just (similar to religious brotherhoods). Further, rather than hiring new members, the Trainers find out and raise children who have been orphaned. Instilled in each member is a strict moral code and belief system surrounding the worship and training of pokemon. Viewed by the world as eccentric at best, the Trainers are renowned for their fighting and training abilities, and employed in any cause they will accept.

Most recently the trainers have been invited to join a war in the North. Groups of raiders have been attacking and pillaging villages and cities along coasts and rivers. They are said to use exclusively water pokemon in a fighting style that is all about striking quickly, pillaging, and retreating back to their ships and out to sea. While raids are not uncommon in the North, the leader of these new bands is said to have a pokemon that is vastly more powerful even than that of kings, and he is using it to murder ever growing numbers of people and pokemon. (Not a huge fan of the story I've set out here and up for suggestions on an alternate plot).

The following is an awesome comic that does a great job putting a very serious and mature mood on a story about pokemon. Additionally the realistic depictions of the pokemon add to the effect. This is the kind of mood I would want establish in this roleplay. Link

Arvalis on deviantart has made tons of realistic pokemon depictions. They are particularly interesting because he has them set next to an outline of a human to show their relative size. Most of them look pretty cool. These are what I'm imagining for the pokemon of our world. Here is a link to his page, just look around in his gallery: (Specifically I'm most impressed with the Evee evoutions, his compilation of all season 1 pokemon, and his Charzard.

Besides those two, a quick search on deviantart and google images for "realistic pokemon brings up a whole slew of images for good inspiration.