So, this isn't technically a chapter, so I am not sure if I am breaking some rule but anyways. If this breaks the rules, PM me and I will take this down.
So, what I had planned for the story? Few things.
First, would have obvious defeat of Discord. This one, I went through numerous ideas.
One idea was for Discord to actually succeed in breaking the final defense line... leading to humans dropping an anti-matter bomb on him. Which would clue everyone else that humans have WMD on the orbit and could, potentially, hit anyone anytime. Which, rather predictably, does not sit well with everyone else, least with Luna. However, as was pointed to me, this was rather stupid idea and was scrapped.
Second idea was similar, once again Discord breaking through but instead of finding source of the Zone, he would encounter prepared Elements of Harmony. However I decided that this was too risky plan and scrapped this one too.
So how would have final version gone? Discord... would have been defeated, turned back into stone, with heavy cost. Dragons and Changelings would become the new boogeymen for humans, as well as general militarization of humans. However, relationships with other nations would be much improved, since they were ready to stand alongside humans.
What of Chryssalis? Well, she has rather complicated position of trying to keep one of few hives in Equestria operational, without drawing ire from Princesses, who are only reason why humans aren't currently embarking on genocide on "bugs".
Also, a lot more stable Equstria. With Princesses showing that they can, indeed, stand up against threats such as Discord anti-Princess sentiment hinted at Luna Aeternal would be decreased. Not disappeared, but would become something you would not mention in public due to shame.
Canon!Celestia would be half appalled of the state of the world and half pitied. However, she would also be optimistic of worlds fate. Canon counterparts would return to their own world, perhaps taking extra time to take a look at the moon... only to find nothing, since humans don't exist in their universe. One twist I thought was to have ruins on the moon in canon universe, with implications that humans died out in some massive civil war. Of course, I decided not to use this, main thing is that Warverse has humans, while canon does not.
Also, one of things that would be hinted, but not yet stated, would be increasing discontent between "Planetbound" and "Moonbound" human factions. Nothing major, but hints for increasing tension that would eventually lead to true human state. Remember, current "state" is more or less still drawing is legitimacy from emergency committee set up back when United Nations used to exist. However, rather than fight pointless war, human government would more or less decide "Screw it." and just accept demands and make reforms, leading to first real democratic elections since Second Human Civil War.
And finally, here is a joke ending I did write, but for understandable reasons I didn't plan to use:
"Now I shall create A WORLD OF CHAOS!"
"How do you make sure it doesn't self-destruct in nuclear fire!?" Twilight pleads
"I shall make sure it doesn't do, while constantly generating more chaos!"
"So, you would be a guardian of balance? An avatar of harmony?"
"... Fuck this" And then Discord was harmony. THE END.
...Maybe I should have gone with that.