[@The Survivor] - Aeons are the entities that fell from the sky, basically. I'm not sure if we're revealing full details about them at this time so I'll hold off for Rockette on that one. 

The war started because monsters appeared alongside the falling of Aeons. These creatures don't care who they attack, they just attack and normal conventions of dealing with threats didn't suffice for these types of beasts, thus SOLDIER. There's also little political battles and others things concerning advanced technology and things we haven't touched on quite yet. 

It's not specifically stated, but considering the Aeons are bonding to the DNA of SOLDIERS through splicing genetic material, I'm not sure that would cause any outer scarring. I'll let Rockette hit that one too.