I think that it is a mistake to plan plots or stories for an RPG, because in my view RPGs are at their best when all the players, GM and character-players alike, are sharing in an extempore collaboration. I reckon that the key technique is to plan conflicts and crucibles, and to let a course of events emerge naturally as character gives rise to incident and incidents arise out of character. So long as characters are steadfast to their natures and everyone avoids jumping conflict a plot will emerge.
Back in the Eighties I did develop a set of techniques for getting PCs to follow a predetermined course of events making up a planned plot; but I gave up using them about 1990 because I found it boring to GM when I didn’t get to extemporise.
As for magic, I am put in mind of a discussion which the Sages of High Wycombe had on the subject of Sanderson’s Laws of Magic, and in particular Sanderson’s First Law. Sanderson points out that an author’s ability to solve conflict with magic is directly proportional to how well the reader understands said magic¹. Readers will not feel satisfied by a story if its conclusion turns on magic doing something that they had no reason to suspect that it could do. The same is true of explaining features of a world. “Magic did it” is not an explanation if magic can and will do things without limits or reason, because it conveys no understanding.
Returning perhaps to a theme, I think it is usually a mistake in RPG to give the players the impression that the world is not amenable to understanding. If the players have no understanding, then the characters have no effective agency; collaboration is impossible.
¹ The same is true of kisses and fistfights, actually. It’s just that we all think we understand kisses and fistfights.