It has been several years, a little over a decade since the famous exploits of teams, from Team Rocket to Team Flare, have ended. There are still criminals out there, but after so many repeated failures in history, none of them are very organized, or if they are, they aren't very big.
In the progression of history, people have received a rude awakening. It seems now that slowly, through the years of peril, and the many different but still similar experiences with these events and criminal teams, Pokemon have gained new awareness of the world. With the long period of calm without these big teams, the knowledge and understanding of the Pokemon has come full circle. They all realize now how people treat them, how they might be friends, or slaves, or tools. Some choose to stand by their trainers no matter what the cost. Some decide to take action against the trainers, and humans altogether, for what they have done. Some still decide to stay neutral, aiding whoever provides the better deal for them.
Where are your pokemon?
In the "Age of Awareness", as it was dubbed by the Pokemon, almost all of them gained the ability to speak as humans do. Pokemon were split between "The Trained" (those who stand by trainers), "The Revolutioneers" (those who fight for Pokemon, and Pokemon alone), and "The Scattered" (those with no purpose to fight for, rogues and those who are neutral).
The Revolutioneers have currently been on a steady rise. In attempt to get more attention, they have made their tactics more ruthless. Their leader, a powerful being unknown to many human eyes, will stop at nothing to achieve his goal, even if it means torturing his own soldiers to keep their support with him.
Any hope now remains with the trainers, and those Pokemon who have still not turned to the darkness in their hearts. Those Pokemon can be found anywhere, and so can those trainers. Who knows? You might find some unlikely allies along the way.
Regardless, only a group-led effort of some kind can bring peace between Pokemon and humans once more, and keep the powers of both from tearing the land asunder...