The story begins with the professor, she was an archaeologist and while exploring a cave where a mystical pokemon were found she was with her crew but suddenly a big blast and it was done by the Evil Team Of The Region (Name Not Decided) and the evil team then manages to catch it. After that incident she was never the same so she became a pokemon professor and wants the character to be played with to fulfill her dreams to fight the evil team and to get the mystical pokemon back safe to place the pokemon lived. But then rival joins hands with the evil team and helps them. So you form a crew to fight against them. In the end you of course win but the evil team is not done yet they will again come back with stronger pokemon and people in the postgame