We could use that. Here is a change.
The main character, Nathan Jones, is from New Dale Town. He just moved here from the Johto Region. As he steps out of his house, a storm is caused. He remembers the news said nothing about a storm. He ignores it and continues on. He tries to leave the town but a girl blocks his way. "You can't leave the town yet, it is to dangerous." She said, soaking from head to toe. Nathan turned around and walked towards the lab. He walks towards the door and it slowly opens. This it so far.
Maka, is going to be intertwined with legendaries, but team terra kidnaps her for a ransom, she has the power to read the thoughts of all pokemon. They are using her to find out the pokemons true intentions. Team Torpedo and Team Shadow team up with Team Terra. The end of the world is caused by a rip in the space time continuom, causing a massive outbreak of pokemon to go wild. Only certain types of pokemon are going wild and there are special pokeballs to stop the madness.
Off the top of my head, and using your story but tweaking it slightly, the main character (Nathan Jones) is from a town. He gains his first Pokemon [insert starter here] and decides to battle his friend, and after the battle, the friend sets off to take on the gym challenge. You decide to do so for yourself, but when you come to a gym, it's a trap. Team Terra steals your best friend, and you decide to look for him/her.
That's my idea of how it starts. I think that Maka should be involved with a few legendary Pokemon (or just some strong and idealist Pokemon). The legendary Pokemon should then cause the end of the world or something and leave you, the main character, to fight them off while saving Maka from the three teams.
The main body should be for searching towns and places for Maka's whereabouts, but it should also be filled with suspense up until the game's conclusion.
But that's just what I think. I also need to know which Pokemon (choices) will the protagonist start with.
I also need to know what you want me to do to help with the project.