There were a small compliment of Legendary pokémon above Mt. Coronet. Rayquaza and Ho-Oh were the center of attention as they debated humanity. Latios, his sister Latias, Articuno and Moltres looked on.
There was a fire in Rayquaza’s eyes as he condemned humanity. Every curse, every foul wish towards the human race was spat out with utter contempt. He showed his disgust with the way humans had enslaved pokémon and used them as nothing but tools and amusement
Rayquaza’s furor finished when he gave his solution.
“Humanity needs to be wiped out from this world.”
Ho-oh retorted. He gave every achievement of their kind to come only with the help of humanity, and he reminded Rayquaza of just how happy many pokémon were with their trainers, and then there was still the most important point to be made.
“It is not your place to decide the future of humanity.”
Rayquaza flew into a rage, releasing a primal roar in the direction of Ho-Oh. Those with the pair quickly chose their alliances - Latios turned and stood at the other dragon’s side, whilst Moltres held his ground with Ho-Oh and Latias slowly edged away from the conflict entirely with Articuno. Ho-Oh stood his ground. Everything stood still for a second that seemed to last forever. The phoenixes charged directly into the the dragons to open the conflict, which ended in a nasty tangle of feathers and scales. Exactly as fast as the conflict began however, it finished as all parties dissipated away from a direct conflict.
The war has now been raging for a year, between the Pokémon Separatists, led by Rayquaza with Latios at his right hand. They consist of the downtrodden, the abused, those that have generally felt the arse-end of humanity. They stand to destroy the human race, the enemy that has enslaved them from day one of their existence. On the other side of the war stand the Loyalists, pokémon that stand to preserve their way of life as it is, for pokémon and humans alike, who are led by Ho-Oh and Moltres.
The war is not going well for the Loyalists. They have been pushed back to Sinnoh, and even in there they only have footholds in Veilstone, Pastoria and Sunyshore. The Wish-Maker is their last chance to save themselves and win this war, but that means the Separatists only have to stop them. Neither side can afford many to assign to finding the Wish-Maker, the Loyalists can't spare anyone who can hold their lines from the Separatists and the Separatists need to maintain their military superiority to the Loyalists or get pushed back. The few that can be spared are your player characters, as you chase down leads and the Wish-Maker itself.