The main character is a boy or a girl living at his or her house. One day when he/she goes out of the house, they stumble upon two adults (one of them in a uniform of some sort and the other seems like a normal character)having a Pokemon battle. You watch with amazement as you see a real Pokemon battle in front of your eyes. The battle ended with the person in the uniform beating the other guy. He runs off, leaving the other stranger who lost behind. When you talk with the stranger, you learn the guy with the uniform just ran of with some important papers.
You go after the person with the uniform. After you get near the place where the stranger with the uniform ran off to, you learn he is with the government and he was only doing his job. The stranger with the uniform was under a mission to get these papers and was successful, he tells you that you could help this government organizations by going on some mission with them. They give you a Pokemon to start and assign you your first mission. You are given specific information to not tell anyone that you are part of this organization.
You take this advance and ask for your first mission. As you go on more missions, you will learn more about the place you are working for. The organization assures you that what your are working for is the best interest for everyone.
Or the pokemon ranger idea
Your a pokemon ranger. At first you go on missions and save pokemon. till one daythe rangers find some legendary pokemon and the ranger bosses true plan is revealed. They are really out to take over whatever region the hack is gonna be in. Then you have to take down the bad pokemon rangers with the help of some other good rangers. It's late ill add more latter I guess...
OR.. a merged Idea(Changes in Bold)
The main character is a boy or a girl living at his or her house. One day when he/she goes out of the house, they stumble upon two adults (one of them in a uniform of some sort and the other seems like a normal character)having a Pokemon battle. You watch with amazement as you see a real Pokemon battle in front of your eyes. The battle ended with the person in the uniform beating the other guy. He runs off, leaving the other stranger who lost behind. When you talk with the stranger, you learn the guy with the uniform just ran of with some important papers. He gives you a pokemon/ you obtained one from earlier
You go after the person with the uniform. After you get near the place where the stranger with the uniform ran off to, you learn he is with the Pokemon Ranger Sqaud and he was only doing his job. The man was under a mission to get these papers and was successful, he tells you that you could help this government organizations by going on some mission with them. But first he must test you, you battle with his pokemon and when you win he takes you to his bosses.
They in turn decide to let you take exams, to see if you are fit/They let you in.
One misson involves you to find the (Insert something here) and you do. You need it to (insert cause here) You do that, and then the rangers bosses swoop in and speed ahead (Finshing the Cause I.E. capturing a legendary). But before they can fully awaken it, you run in and battle them. They run off/Are taken away by the other organization. And then you capture the legendary.