Try making an outline of the entire plot to your story, and then slowly subdivide it.
Like
-Game begins
-Truth is realized. Storyline is revealed as having a much greater scope than originally thought.
-Powers are given. Hero realizes who he really is, and what he is truly capable of.
-Final Battle
And then tackle each part individually.
-Game begins. Why? How? For what reason?
--Hero has no idea what's going on.
--Routine missions for a bit and then hell breaks loose.
And then expand on those, separately.
-Game beings
--Hero has no idea what's going on.
---He's an oblivious grunt who is unknowingly helping the enemy.
---How did he get there? How long will he be there?
--Routine missions for a bit, and then hell breaks loose.
---Hero feels something is wrong.
---Escape from the enemies' hands and start your own adventure.
---Where does he go next? Why?
I'm not giving the best examples, I suppose, but I think you know what I mean.
Before I even started on my game (which I am not going to finish in RPGMaker, but whatever) I had a TON of word and notepad files about characters, and specifics on the storyline, the setting, even files about specific scenes that I came up with that I didn't want to forget. But I had one HUGE file that outlines the entire story. Not all of it, but bits and pieces that I kept expanding and detailing as time went on. And THEN I started using RPGMaker.