Rebellious Ambitions

Prologue:
Over 40 years ago, mysterious unknown (at the time) forces assaulted the regions of Kanto, Sinnoh, Johto, and Hoenn. The night it happened is still clear as day to all those where were present or involved at the time. . .
Citizens of Goldenrod were rudely awakened when they heard sudden explosions and saw an army of mysterious people clad in black raiding the city. A good majority of the trainer, upon seeing the ituation at hand, immediately sent out their Pokémon as some of them escaped to the radio tower.
Johto wasn't the only one experiencing this strange phenomenon. Kanto was facing the same exact problem while Hoenn was facing off two different groups who were (surprisingly) working together for once in their life; one group clad in red while the other was clad in blue. . .
Sinnoh was facing the same predicament as the other regions, battling a group clad in white and black. All groups in all regions appeared to be heading towards the radio towers. . .
Meanwhile, the trainers were holding their own against the mysterious forces. But it wasn't long until all the enemies had successfully raided the towers and sent a broadcast worldwide.
"Attention, everyone!" one of the guys from each region shouted. "We are Team Rocket, Magma Aqua, and Galactic! And we are here to take over the world! All trainers currently battling must back down now, or face the consequences!" As if on cue, some of the grunts took out their stronger Pokémon and they readied their attacks as if to prove their point. "From this moment on, the regions of Kanto, Johto, Hoenn, and Sinnoh are officially under our control."
As the years passed people showed less and less resistance, as they didn't know what the "new rulers" were capable of. However, within the regions, several people secretly set up gyms for trainers eager to stop these evil teams to take on allowing special badges to boost a Pokémon's power if they can win. What the evil teams did not know, was that their over 40 year reign will soon come to an end. . .