I hope the silent protagonist's name isn't Arsenic also. That could get redundant.
Either your intro leaves quite a lot out, or your plot as it is now really doesn't hold water. It has the potential to be solid, but you'd have to come up with convincing reasons for Professor Ben (is that a nod to Pokemon Brown?) to be concocting a legendary in his small-time lab, presumably with the help of at most two aides, and for Cooltrainer Arsenic to be so vengeful (being related to the professor would help there), among other implausible things. What is Ben going to do with this legendary? What exactly does Team Rocket do that scars the protagonist so badly?
I suggest you start with the legendary; come up with some solid background for it, like the purpose of its existence and stuff like that -- something beyond "because legendaries are cool and make good plot points". It seems to be the main variable in the motives of all your characters, so it should be important to the story in a logical way.