First, you may want to read this topic since this idea has something related to RC or stuff that can make Pokemon stronger in illegal ways.
http://pokemon-universe.com/index.php/topic,3986.0.html

In the Miryus region, an evil organization (insert evil organization name here) has started their actions to become the ruler for not just Miryus region, but the entire world. They steal, abuse, smuggle, kidnap Pokemon and people, and doing other evil movements in order to fulfill their ambition.

Many people in the Miryus region become a trainer because the story of success of the legendary Pkmn Trainer Red (He's awesome and badass). Red is rumored to be very powerful, every Pokemon he trained will become the strongest of its kinds. However, no one ever seen him in many years, some people said Red is traveling the world, train more Pokemon, looking for legendary Pokemons, and other reason that can fit the mystery of Red disappearances.
Those good rumors turned into real bad, when another rumor appeared that the evil organization is doing research and experiment that can infect control over many Pokemon, and also make them brutally stronger than usual. Red is suspected as the organization leader because of this new rumor.

After a few months, the evil organization's hideout is found in the mountains. All the elite trainers, including you/player/protagonist/whatever you call it, gym leaders, and even the Pokemon League Elite Four and Champion are ambushing the hideout to put an end to their evil ambitions. The group of all those trainers are called "Pokemon Trainer Alliance Forces" or PTAF fo short (if you had better names, just mention it).
The fight between the good and evil is long, harsh, and unexpected for the good side. The evil organization has infected many wild Pokemon around the mountains, turning them into unconsciously battling machines for the organization. Some trap has been set so that the virus can spread and infect the PTAF's pokemons, causing them to strike back their own trainers.

After the both side were exhausted from the long battle. The leader along with the admins came out from the Central Hideout Laboratory. Surprisingly, the organization leader was the professor who worked together with Professor Alder, he helped you to create new medicines and pokeballs to capture and cure the pokemons infected with the virus of the organization. (Insert name for the organization leader here) announced that PTAF's attempt to stop the organization is useless, the virus he invented will be perfect in a short time. The virus will no longer has a cure, it will give infected pokemon more power, and they will obey him (the organization leader) for the rest of their life.

All of sudden, one of the admin standing next to the leader sent out a Pikachu and tries to attack the leader. Too bad, the other admins sent out a Manectric and absorb the Pikachu's thunderbolt. It was Red! He then battles the admins, while the leader quickly fled to the Central Hideout Laboratory. The PTAF's now rises, and counter-attack the organization. Everyone tries to reach the Central Hideout Laboratory, but only you managed to slip through the guard and enters the Central Hideout Laboratory with your pokemon...
And the final battle begins.

Well, I guess that's all for now, I'll continue later because my hands are tired of typing, and I hoped you liked it