"Magic" System Issues

As I write and flesh out my story I've run into many little problems along the way. Most of them are minor, like I have my main character chasing off in one direction and then he's over there... How did he get there? That was easily fixed by adding in a scene in which I took the opportunity to give more insight into his personality and relationships with those around him.

Unfortunately the issue of how my magic system works has taken a truck hauling monkey wrenches and dumped it on my story. Then for good measure it crashed the truck into the pile and set it on fire.Perhaps it is not that bad, but it has certainly stumped me. Also, I am using "magic" as a generic term since it encompasses all the outside of them norm or "fantastical" system, like technology and powers and magic.

I have set up what the magics of my world are; how they work, their limitations, and other details for how the system interacts with the environment, characters, and story. But then I ran into a wall in the form of a question: Where did this magic come from and why do certain people have them while others do not? I just looked at my computer screen and shrugged, You tell me! Neither my story nor my computer responded, very rude of them both in my opinion.

Where did the magic come from? My story is already set to follow a few years after the end of a war that was started because of the magic, so I have a starting point. The magic came before the war era and other things spawned into existence during the war because of them or to counter them. Something happened (or didn't) and people became special while others did not. This leads to friction and animosity, and ultimately war.

So there is a pretty set when, but still no how. The few ideas I've come up with are: it just is, space stuff, nuclear stuff, genetic engineering, a rift between dimensions, or perhaps different environmental factors that culminated into some people being "lucky" enough to be born with magic. There are a few other ideas, but those are the leaders and each offers some interesting aspects, but the issue of making it believable becomes the new issue. That last one is the easier of solutions I've thought of and I am leaning towards it. On the Pro side, it solves the problem and I my system essentially just-is. On the Con side, at face-value, my system could be interpreted as a Marvel mutants knock-off.

All of the ideas I have come up with so far are definitely workable, but I want it to be more than a footnote that says to the reader "This is how, move along, these aren't the droids you're looking for". I want my system to be fun, entwined in the world and story not simply background, and at the forefront I want it to be believable. I want readers to want to be apart of it too, the same way the books I've read have drawn me in.

Certainly more thought and research is required before I commit to the origin of my system.

-Tony