Nobody replied yet? That's kinda sad...
After choosing you go to your house to show your parents before going back to the lab to get the rest of the supplies.
When you go back to the lab a gang of trainers kidnap Maple Figures.... You try to help, but they are too strong So why don't they kidnap you, too? The more, the merrier, right?.
You wake the next morning at home because you passed out. You get an email from the ETU (Elite Trainers Unit) to help find professor Maple If you're a beginner, why would you be affliated with a bunch of elites? I'd bet they'd have at least one badge.... Excited you travel to Solon City to join. After join you embark on a long journey where you find Maple, but you have to fight the Gang sub leader. They release her, but you learn of their plan to use Mewtwo and Mew to form the Physic Square xD a force of Pokémon capable to destroy the ones in existence. How do they know of this Physic Square? It can't be an 'ancient power' because Metwo is synthetic...and why would Mewtwo and Mew go along with this, anyways? They ARE sentient beings in addition to being powerful Psychic types...not to mention how would they be found? If the Professor knew of the Physic Square, then why wouldn't s/he just make it him or herself?
You tell the ETU about this, and you get to join a search party for the gang.
You track them to the Silus region where you find the gang. But it’s too late! The gang use the physic square to combine the Pokémon to make cross breeds ...you mean like a Dialgia? Cool, make sure to get me one, 'kay?!
You now lead Are all of the elitists gone? I highly doubt you're at the top of the organisation... a harder mission, to find something A relic? An amulet? A GS Ball? able to stop these cross breeds and save the people from the gang it’s up to you and the ETU!
This isn't the full story! I know; that's why I asked several questions.