The story isn't a complicated one. You want to become the best Pokemon trainer which you accomplish by traipsing with your Pokémons around Johto and Kanto. It's probably best to make up your own motivation. Maybe your mother has a terrible bone-eating disease and you must raise enough money for her cure. Or you are intent on world domination by creating a fierce army of Pokémon. Oh yes, those rapscallions of Team Rocket are back causing trouble, but it's a minor sideplot.