I would suggest that before you go any further into that huge concept of story and game that you take your time and first get use to the basic of RPGMAKER like first start doing an easy sceen where you have your hero opening a door or a chest and winning an object using switch then give yourself some challenge by trying to make harder stuff like simulate an escalator. Just make sure you master every aspect of RPG maker before trying to create games.
My suggestion is that you think about an easy senario with let say 5 quest, 1 town, 1 dongeon, 2 characters(1 then a second one join in later in your senario), Create at least the following: 1 weapon shop, 1 armor shop, 1 item shop and finaly a inn.
Set up the fights for outside the town and inside your dongeon, Create a final boss at the end of your dongeon and before that of course a couple chest inside the dongeon with great weapons and armors to help your hero's kill the final boss.
Once you will have create all that by yourself, then you will be way out of the "I'M SO NOOBISH PLEASE HELP ME TO DO MY RPG BY DOING IT ALL YOURSELF FOR ME!"
I'll be the first one to help you out when you will need too but first you need to learn how to walk before running or ask to be lifted out to where you wanna go.
Keep up the good work and of course take this comment as constructive and see there a friend trying to help you and not someone judging you.
Hope this will help!
Elistios