What's the story you've always dreamt of telling? Tell that one. Don't worry if it's cliche, don't worry if it's been done before, make the game you want to make.
However, if you're just starting out with rpgmaker, I'd recommend starting really
really small. I would aim for a short game about an hour long. For the sake of this post, let's say that's what you're doing.
Now that we know what kind of game were making, we can flesh out the story. Since our game is only an hour long, we really don't have the time for an epic story, so let's think small. The first thing that popped into my mind while writing this post was a Smuggler. Maybe you're sneaking goods out for a city, and get caught - now you have to fight through the city and make it out with as much gold as possible.
I'm sure if you think about this idea, a bunch of game mechanics will pop into your head as well, and that's how a game story comes to be.
So to summarize: Identify your scope, and stick with it. Find an idea that you love, whether it be a particular character or a world that you created. Take a bite size portion of that character (a moment in their life) or world (a historic event)and write a small story about it.
However, there are far more intricacies when it comes to longer games. Branching stories that intertwine and then end abruptly, choices that affect gameplay, and each character's personality. This doesn't even begin to tackle lore, dialogue, or skill and item descriptions.
If you're trying to write a story for a large game, you'll definitely be undertaking an immense task. Luckily, you're on the right forum!