heres a bit of the story:
Team Aqua and Team Magma join forces and create Team Steam (gettit?) and they attempt to control the world by awakening and controlling the three legendary, mythical pokemon. Yeah its a big, fat cliche i know, but how about this. They succeed and rule over Hoenn to start with and spread to Johto and then to Kanto. It's upto you to foil their attempt to rule your home region but the only way to do it is to capture the right Pokemon that will help you as well as the two peace makers (mewtwo,mew lugia,celebi Jirachi,deoxys that sort of thing) and then have the ultimate battle with the entire world at stake.
This will happen during the second half of the game though as you have all the gyms to work through first...