Worldbuilding

As I mentioned over at the Water Cooler, I'm in the process of creating a comic for a nuzlocke run and thought it'd be a good idea to toss around some ideas and theories and the like. The nuzlocke is based in Hoenn, but will deal with the other regions too, specifically Johto and Kanto. Some of you may know about the war theories that float around on the internet, but I kinda want a more original one. Basically, the question I'm trying to figure out is what the war was about. I've decided that it'd be a civil war between Johto and Kanto, and Hoenn allied up with Johto, but over what issue? What do you guys think when you hear 'civil war'?

Magma vs. Aqua.

I just realized I should have said its a past war, so Magma and Aqua haven't clashed yet I'm thinking the war would have ended about 10-15 years before the time of the nuzlocke run :P

I don't know many of the theories going around the internet, but if were dealing with a civil war which means the regions of "Jhoto" and "Kanto" are one nation ((unless I'm really derping on the definition of civil war)). The civil war could be what divide the nation into the smaller regions. Though I'm not quite sure what the conflict would be. Maybe because the region was so big one side felt that it wasn't being well represent. Social injustice or economic problems are some other ideas. (if it's not a civil war it could be about land or something).

Whatever that war was over, it's worth pointing out that it doesn't come up very much in the official games, if at all. So it was probably even earlier, or over a matter nobody wants to talk about.

Oh wait, are we talking about the actual war or a war for AU ideas?

AU ideas.

There's no indication that there was any civil war in the games; the closest there is is Lt. Surge's vague reference to "the war" where electric Pokémon saved his life.