The other day I saw a discussion going on about GM prep and whether or not pre-planning your plot would interfere with player agency. The idea being that the more you develop the plot the less the players could impact it, and thus the less agency they have. It's a simple concern, but one born not so much out of evidence as a misunderstanding. See, the advice isn't to pre-plan the story it is to pre-plan the Plot. The difference between a plot and a story is the key thing here.
Ok, Smarty-pants, what is the difference?
The biggest difference to the Plot and the Story is that the story is the sequence of events that relates what happens while the Plot is the Cause and Effect that allows that story to happen. Not with me? Think of it where the Plot is the skeleton of a body, while the story is the muscle, flesh, and spirit of the person that the skeleton is the basis of.
Another example? Ok, well look to Star Wars
Story: Luke goes out into the desert, finds R2-D2, gets attacked by Sand People, and meets Ben Kenobi.
Plot: because Luke doesn't want to get in trouble for losing R2-D2 he goes after him. He tracks R2-D2 to the desert and follows. R2 notes nearby people so Luke goes to look and finds Sand People who attack him.
See it now? The Plot has the Cause and Effect of it, but the choice is still the characters. And that is what is important.
Plot Sets Up The Conflict, Story Is How The Character Deals With It
That line right there might be a better explanation for the difference, and it also shows how preparing for the one doesn't prevent the other.
As a GM you want to have the plot prepared. Plot is how the world moves to cause the problems that will give the Players their adventure and story. You need to have this going forward.
What About Agency?
Look at the previous line. Where is Agency impacted? Plot is presenting the choice, the Players then choose how to deal with that problem. They have all the agency they could have or want right there. Plus, with focusing on plot, you will have a better story anyhow.
How Does That Work?
Like I said, plot is about cause and effect. For example:
Because he wants to rule the world the evil wizard M has assembled a dark army and is marching on the countries around his home of Idranay.
Because the surrounding kingdoms don't want to be conquered they are raising their own armies to march and meet M's army.
So what do the PCs do? They're in those kingdoms. Armies are being recruited. Their very lives are at stake. Do they join up with the army? Or do they do something else? If they do something else, what is it and how do they do it?
The fun part is that even if the PCs don't engage with that plot doesn't mean it goes away. Perhaps they engage with the "Lady Miriam needs 5 deer capes by three pm on Tuesday" for now. Perhaps they do other plots after that. That big plot though doesn't go away. It just comes to find them eventually, either as a victory for the good guys and lost glory for the PCs, or, more likely, as victory for M and the dark armies being even closer.