I guess so, I like the idea of rayquaza becoming corrupted, and how giritna is involved, because he can keep the remaining souls in a corrupted reverse world (like the final dungeon i guess) okay so let me make sense of this, whilst adding some cool new stuff.
500 years ago there was a war, and the war raged on for a few years, putting the region into poverty, and many pokémon became outlaws, or bad pokémon, in hope for a chance of survival. The weak were killed and the strong became bad, then there was the good, the four teams of [region.] The four teams joined together in hope of surviving and helping the war, or to put an end to it. Everything seemed to be working for the better, as the war settled for a little while, for pokémon to repopulate, and try and make a suitable living envirement. many pokémon decided to live under the ground, or into the mountain's in hope that they wouldn't be spotted, and the sea pokémon carried on as usual, as they hadn't been effected too much. However, after 2 years of nothing, rayquaza emerged, who was curious as to why the war had stopped, as he had previously wanted to help out. Then darkrai appeared before him, and told him lies and tricked rayquaza into believing that the world had abandoned him, and didn't want his help anymore. Rayquaza was frustrated, because he thought that the pokémon below were more powerful than he was, and soon teamed up with giritina, promising him that he would be free from the distortion world once he had helped rayquaza out. Giritina used is power to manipulate and distort the minds of several areas of pokémon, which were to join the war effort, and work for rayquaza uncontrollobly, and rayquaza enjoyed it so much, the feeling of war, that he became uncontrollable - black rayquaza. Soon a large scale, but not to lengthy war (50 days) occured, and was quickly sorted out by jirachi, who had been woken up by celebi from a year in the future. The jirachi was then sent to confront rayquaza, with celebi at it's side, (the two are friends) and rayquaza first listened to what jirachi had to say, but declined, for he wanted war so much now. he koncoked juirachi out the way, and celebi quickly went to save her friend, and teleported a year back to the future in order for jirachi to regain his strength. Rayquaza knew that he was to return, so he quickly ordered giritina to make him stronger. Giritina started to take away the souls of pokémon, but only lasted roughly a day before jirachi's return, this time there was no holding back. Jirachi made the wish, and Celebi set the time scale for 100 years, but due to rayquaza's newly found power, it seemed as though 500 years was more acurate. The war subsided. rayquaza was sent back to the ozone layer, where he would sleep for 500 years. Little did the pokémon that rejoiced down below know, giritina was still around, and pokémon, little by little, began to disapeer, with no trace, and fed the souls to black rayquaza. The pokémon below were informed of jirachi and celebi's doing, and were congratulated by everyone, even lugia, who was passing by, just by chance. Soon Celebi, and Jirachi were made icons of the region, but they knew everything wasn't over just yet. They knew they didn't want the public to panic, so they instructed the famous guild [thats us yay] to gather up defences in any way possible. Jirachi went to sleep for another 600 years in the Hoenn region, and Celebi promised it would be back, and hopefully with Dialga. Everything seemed in order, but there were still bad pokémon around and a mission set. And thats where our story begins.
Hows that?